diff --git a/.changeset/add-prune-option.md b/.changeset/add-prune-option.md
new file mode 100644
index 000000000..62e9fc059
--- /dev/null
+++ b/.changeset/add-prune-option.md
@@ -0,0 +1,13 @@
+---
+"counterfact": minor
+---
+
+Added `--prune` option to remove route files that no longer exist in the OpenAPI spec.
+
+When an OpenAPI spec renames a path parameter (e.g. `/pet/{id}/update/{Name}` → `/pet/{id}/update/{nickname}`), running without `--prune` leaves the old file in place alongside the newly generated one, causing wildcard ambiguity in route matching. The new flag cleans up defunct route files before generation runs.
+
+```sh
+npx counterfact openapi.yaml ./out --generate --prune
+```
+
+Context files (`_.context.ts`) and empty directories are handled correctly — context files are never pruned, and any directories left empty after pruning are removed automatically.
diff --git a/bin/counterfact.js b/bin/counterfact.js
index 50fccdb9a..b0c4d25cc 100755
--- a/bin/counterfact.js
+++ b/bin/counterfact.js
@@ -155,6 +155,8 @@ async function main(source, destination) {
         options.watch ||
         options.watchTypes ||
         options.buildCache,
+
+      prune: Boolean(options.prune),
     },
 
     openApiPath: source,
@@ -326,5 +328,9 @@ program
     "--always-fake-optionals",
     "random responses will include optional fields",
   )
+  .option(
+    "--prune",
+    "remove route files that no longer exist in the OpenAPI spec",
+  )
   .action(main)
   .parse(process.argv);
diff --git a/src/server/config.ts b/src/server/config.ts
index 6e39cf371..7f2aa316c 100644
--- a/src/server/config.ts
+++ b/src/server/config.ts
@@ -4,6 +4,7 @@ export interface Config {
   basePath: string;
   buildCache: boolean;
   generate: {
+    prune?: boolean;
     routes: boolean;
     types: boolean;
   };
diff --git a/src/typescript-generator/code-generator.ts b/src/typescript-generator/code-generator.ts
index 45487db56..445eb7ee0 100644
--- a/src/typescript-generator/code-generator.ts
+++ b/src/typescript-generator/code-generator.ts
@@ -9,14 +9,18 @@ export class CodeGenerator extends EventTarget {
 
   private readonly destination: string;
 
-  private readonly generateOptions: { routes: boolean; types: boolean };
+  private readonly generateOptions: {
+    prune?: boolean;
+    routes: boolean;
+    types: boolean;
+  };
 
   private watcher: FSWatcher | undefined;
 
   public constructor(
     openApiPath: string,
     destination: string,
-    generateOptions: { routes: boolean; types: boolean },
+    generateOptions: { prune?: boolean; routes: boolean; types: boolean },
   ) {
     super();
     this.openapiPath = openApiPath;
diff --git a/src/typescript-generator/generate.js b/src/typescript-generator/generate.js
index 37be6b3f2..4ec0eef4c 100644
--- a/src/typescript-generator/generate.js
+++ b/src/typescript-generator/generate.js
@@ -7,6 +7,7 @@ import createDebug from "debug";
 
 import { ensureDirectoryExists } from "../util/ensure-directory-exists.js";
 import { OperationCoder } from "./operation-coder.js";
+import { pruneRoutes } from "./prune.js";
 import { Repository } from "./repository.js";
 import { Specification } from "./specification.js";
 
@@ -72,6 +73,12 @@ export async function generate(
 
   debug("got %i paths", paths.size);
 
+  if (generateOptions.prune && generateOptions.routes) {
+    debug("pruning defunct route files");
+    await pruneRoutes(destination, paths.keys());
+    debug("done pruning");
+  }
+
   const securityRequirement = specification.getRequirement(
     "#/components/securitySchemes",
   );
diff --git a/src/typescript-generator/prune.js b/src/typescript-generator/prune.js
new file mode 100644
index 000000000..4905dc862
--- /dev/null
+++ b/src/typescript-generator/prune.js
@@ -0,0 +1,127 @@
+import fs from "node:fs/promises";
+import nodePath from "node:path";
+
+import createDebug from "debug";
+
+const debug = createDebug("counterfact:typescript-generator:prune");
+
+/**
+ * Collects all .ts route files in a directory recursively.
+ * Context files (_.context.ts) are excluded.
+ * @param {string} routesDir - Path to routes directory
+ * @param {string} currentPath - Current subdirectory being processed (relative to routesDir)
+ * @returns {Promise<string[]>} - Array of relative paths (using forward slashes)
+ */
+async function collectRouteFiles(routesDir, currentPath = "") {
+  const files = [];
+
+  try {
+    const fullDir = currentPath
+      ? nodePath.join(routesDir, currentPath)
+      : routesDir;
+    const entries = await fs.readdir(fullDir, { withFileTypes: true });
+
+    for (const entry of entries) {
+      const relativePath = currentPath
+        ? `${currentPath}/${entry.name}`
+        : entry.name;
+
+      if (entry.isDirectory()) {
+        files.push(...(await collectRouteFiles(routesDir, relativePath)));
+      } else if (entry.name.endsWith(".ts") && entry.name !== "_.context.ts") {
+        files.push(relativePath);
+      }
+    }
+  } catch (error) {
+    if (error.code !== "ENOENT") {
+      throw error;
+    }
+  }
+
+  return files;
+}
+
+/**
+ * Recursively removes empty directories under rootDir, but not rootDir itself.
+ * @param {string} dir - Directory to check
+ * @param {string} rootDir - Root directory that should never be removed
+ */
+async function removeEmptyDirectories(dir, rootDir) {
+  let entries;
+
+  try {
+    entries = await fs.readdir(dir, { withFileTypes: true });
+  } catch {
+    return;
+  }
+
+  for (const entry of entries) {
+    if (entry.isDirectory()) {
+      await removeEmptyDirectories(nodePath.join(dir, entry.name), rootDir);
+    }
+  }
+
+  if (nodePath.resolve(dir) === nodePath.resolve(rootDir)) {
+    return;
+  }
+
+  const remaining = await fs.readdir(dir);
+
+  if (remaining.length === 0) {
+    await fs.rmdir(dir);
+    debug("removed empty directory: %s", dir);
+  }
+}
+
+/**
+ * Converts an OpenAPI path to the expected route file path (relative to routesDir).
+ * e.g. "/pet/{id}" -> "pet/{id}.ts", "/" -> "index.ts"
+ * @param {string} openApiPath
+ * @returns {string}
+ */
+function openApiPathToRouteFile(openApiPath) {
+  const filePath = openApiPath === "/" ? "index" : openApiPath.slice(1);
+
+  return `${filePath}.ts`;
+}
+
+/**
+ * Prunes route files that no longer correspond to any path in the OpenAPI spec.
+ * Context files (_.context.ts) are never pruned.
+ * @param {string} destination - Base destination directory (contains the routes/ sub-directory)
+ * @param {Iterable<string>} openApiPaths - Iterable of OpenAPI path strings (e.g. "/pet/{id}")
+ * @returns {Promise<number>} - Number of files removed
+ */
+export async function pruneRoutes(destination, openApiPaths) {
+  const routesDir = nodePath.join(destination, "routes");
+
+  const expectedFiles = new Set(
+    Array.from(openApiPaths).map(openApiPathToRouteFile),
+  );
+
+  debug("expected route files: %o", Array.from(expectedFiles));
+
+  const actualFiles = await collectRouteFiles(routesDir);
+
+  debug("actual route files: %o", actualFiles);
+
+  let prunedCount = 0;
+
+  for (const file of actualFiles) {
+    const normalizedFile = file.replaceAll("\\", "/");
+
+    if (!expectedFiles.has(normalizedFile)) {
+      const fullPath = nodePath.join(routesDir, file);
+
+      debug("pruning %s", fullPath);
+      await fs.rm(fullPath);
+      prunedCount++;
+    }
+  }
+
+  await removeEmptyDirectories(routesDir, routesDir);
+
+  debug("pruned %d files", prunedCount);
+
+  return prunedCount;
+}
diff --git a/test/typescript-generator/prune.test.js b/test/typescript-generator/prune.test.js
new file mode 100644
index 000000000..326b18a9e
--- /dev/null
+++ b/test/typescript-generator/prune.test.js
@@ -0,0 +1,125 @@
+import { describe, expect, it } from "@jest/globals";
+import { promises as fs } from "node:fs";
+import path from "node:path";
+
+import { pruneRoutes } from "../../src/typescript-generator/prune.js";
+import { withTemporaryFiles } from "../lib/with-temporary-files.ts";
+
+describe("pruneRoutes", () => {
+  it("removes a route file that is not in the OpenAPI spec", async () => {
+    await withTemporaryFiles(
+      {
+        "routes/pet/{id}.ts": "export const GET = () => ({ status: 200 });",
+        "routes/pet/{name}.ts": "export const GET = () => ({ status: 200 });",
+      },
+      async (basePath, { path: getPath }) => {
+        const expectedPaths = ["/pet/{id}"];
+        const count = await pruneRoutes(basePath, expectedPaths);
+
+        expect(count).toBe(1);
+        await expect(
+          fs.access(getPath("routes/pet/{id}.ts")),
+        ).resolves.toBeUndefined();
+        await expect(
+          fs.access(getPath("routes/pet/{name}.ts")),
+        ).rejects.toThrow();
+      },
+    );
+  });
+
+  it("keeps context files even when not in the spec", async () => {
+    await withTemporaryFiles(
+      {
+        "routes/_.context.ts": "export class Context {}",
+        "routes/pet/_.context.ts": "export class Context {}",
+        "routes/pet/{id}.ts": "export const GET = () => ({ status: 200 });",
+      },
+      async (basePath, { path: getPath }) => {
+        const expectedPaths = ["/pet/{id}"];
+        const count = await pruneRoutes(basePath, expectedPaths);
+
+        expect(count).toBe(0);
+        await expect(
+          fs.access(getPath("routes/_.context.ts")),
+        ).resolves.toBeUndefined();
+        await expect(
+          fs.access(getPath("routes/pet/_.context.ts")),
+        ).resolves.toBeUndefined();
+      },
+    );
+  });
+
+  it("removes empty directories after pruning", async () => {
+    await withTemporaryFiles(
+      {
+        "routes/old/{id}.ts": "export const GET = () => ({ status: 200 });",
+      },
+      async (basePath, { path: getPath }) => {
+        const expectedPaths = [];
+        await pruneRoutes(basePath, expectedPaths);
+
+        await expect(fs.access(getPath("routes/old"))).rejects.toThrow();
+      },
+    );
+  });
+
+  it("does not remove directories that still contain context files", async () => {
+    await withTemporaryFiles(
+      {
+        "routes/old/{id}.ts": "export const GET = () => ({ status: 200 });",
+        "routes/old/_.context.ts": "export class Context {}",
+      },
+      async (basePath, { path: getPath }) => {
+        const expectedPaths = [];
+        await pruneRoutes(basePath, expectedPaths);
+
+        await expect(fs.access(getPath("routes/old"))).resolves.toBeUndefined();
+        await expect(
+          fs.access(getPath("routes/old/_.context.ts")),
+        ).resolves.toBeUndefined();
+      },
+    );
+  });
+
+  it("handles the root path '/'", async () => {
+    await withTemporaryFiles(
+      {
+        "routes/index.ts": "export const GET = () => ({ status: 200 });",
+        "routes/old.ts": "export const GET = () => ({ status: 200 });",
+      },
+      async (basePath, { path: getPath }) => {
+        const expectedPaths = ["/"];
+        const count = await pruneRoutes(basePath, expectedPaths);
+
+        expect(count).toBe(1);
+        await expect(
+          fs.access(getPath("routes/index.ts")),
+        ).resolves.toBeUndefined();
+        await expect(fs.access(getPath("routes/old.ts"))).rejects.toThrow();
+      },
+    );
+  });
+
+  it("returns 0 when all files match the spec", async () => {
+    await withTemporaryFiles(
+      {
+        "routes/pet/{id}.ts": "export const GET = () => ({ status: 200 });",
+        "routes/pet.ts": "export const GET = () => ({ status: 200 });",
+      },
+      async (basePath) => {
+        const expectedPaths = ["/pet/{id}", "/pet"];
+        const count = await pruneRoutes(basePath, expectedPaths);
+
+        expect(count).toBe(0);
+      },
+    );
+  });
+
+  it("returns 0 when the routes directory does not exist", async () => {
+    await withTemporaryFiles({}, async (basePath) => {
+      const count = await pruneRoutes(basePath, ["/pet/{id}"]);
+
+      expect(count).toBe(0);
+    });
+  });
+});