diff --git a/src/core/tools/__tests__/readFileTool.spec.ts b/src/core/tools/__tests__/readFileTool.spec.ts
index 44be1d3b924..b79ac269b96 100644
--- a/src/core/tools/__tests__/readFileTool.spec.ts
+++ b/src/core/tools/__tests__/readFileTool.spec.ts
@@ -481,6 +481,36 @@ describe("read_file tool XML output structure", () => {
 				`<files>\n<file><path>${testFilePath}</path>\n<content/><notice>File is empty</notice>\n</file>\n</files>`,
 			)
 		})
+
+		it("should treat files with only BOM as empty", async () => {
+			// Setup - file has BOM only
+			mockedCountFileLines.mockResolvedValue(1) // File has 1 line
+			mockedExtractTextFromFile.mockResolvedValue("\uFEFF") // Only BOM
+			mockProvider.getState.mockResolvedValue({ maxReadFileLine: -1 })
+
+			// Execute
+			const result = await executeReadFileTool({}, { totalLines: 1 })
+
+			// Verify - should show empty file notice since BOM is stripped
+			expect(result).toBe(
+				`<files>\n<file><path>${testFilePath}</path>\n<content/><notice>File is empty</notice>\n</file>\n</files>`,
+			)
+		})
+
+		it("should strip BOM from file content", async () => {
+			// Setup - file has BOM followed by content
+			mockedCountFileLines.mockResolvedValue(1)
+			mockedExtractTextFromFile.mockResolvedValue("1 | \uFEFFHello World") // BOM + content with line number
+			mockProvider.getState.mockResolvedValue({ maxReadFileLine: -1 })
+
+			// Execute
+			const result = await executeReadFileTool({}, { totalLines: 1 })
+
+			// Verify - BOM should be stripped from the content
+			expect(result).toBe(
+				`<files>\n<file><path>${testFilePath}</path>\n<content lines="1-1">\n1 | \uFEFFHello World</content>\n</file>\n</files>`,
+			)
+		})
 	})
 
 	describe("Error Handling Tests", () => {
diff --git a/src/core/tools/readFileTool.ts b/src/core/tools/readFileTool.ts
index 6de8dd56421..0cc196bce1e 100644
--- a/src/core/tools/readFileTool.ts
+++ b/src/core/tools/readFileTool.ts
@@ -519,9 +519,14 @@ export async function readFileTool(
 				// Handle normal file read
 				const content = await extractTextFromFile(fullPath)
 				const lineRangeAttr = ` lines="1-${totalLines}"`
-				let xmlInfo = totalLines > 0 ? `<content${lineRangeAttr}>\n${content}</content>\n` : `<content/>`
 
-				if (totalLines === 0) {
+				// Check if file is effectively empty (no lines, only whitespace, or only BOM)
+				// Note: BOM is already stripped by extractTextFromFile
+				const isEffectivelyEmpty = totalLines === 0 || content.trim() === ""
+
+				let xmlInfo = !isEffectivelyEmpty ? `<content${lineRangeAttr}>\n${content}</content>\n` : `<content/>`
+
+				if (isEffectivelyEmpty) {
 					xmlInfo += `<notice>File is empty</notice>\n`
 				}
 
diff --git a/src/integrations/misc/extract-text.ts b/src/integrations/misc/extract-text.ts
index 8c7e7408a68..b7011dd172e 100644
--- a/src/integrations/misc/extract-text.ts
+++ b/src/integrations/misc/extract-text.ts
@@ -5,6 +5,7 @@ import mammoth from "mammoth"
 import fs from "fs/promises"
 import { isBinaryFile } from "isbinaryfile"
 import { extractTextFromXLSX } from "./extract-text-from-xlsx"
+import stripBom from "strip-bom"
 
 async function extractTextFromPDF(filePath: string): Promise<string> {
 	const dataBuffer = await fs.readFile(filePath)
@@ -67,7 +68,9 @@ export async function extractTextFromFile(filePath: string): Promise<string> {
 	const isBinary = await isBinaryFile(filePath).catch(() => false)
 
 	if (!isBinary) {
-		return addLineNumbers(await fs.readFile(filePath, "utf8"))
+		const content = await fs.readFile(filePath, "utf8")
+		// Strip BOM if present before adding line numbers
+		return addLineNumbers(stripBom(content))
 	} else {
 		throw new Error(`Cannot read text for file type: ${fileExtension}`)
 	}
diff --git a/src/integrations/misc/read-lines.ts b/src/integrations/misc/read-lines.ts
index 5a5eda9f838..2d9d1e9a22c 100644
--- a/src/integrations/misc/read-lines.ts
+++ b/src/integrations/misc/read-lines.ts
@@ -7,6 +7,7 @@
  * Now you can read a range of lines from a file
  */
 import { createReadStream } from "fs"
+import stripBom from "strip-bom"
 
 const outOfRangeError = (filepath: string, n: number) => {
 	return new RangeError(`Line with index ${n} does not exist in '${filepath}'. Note that line indexing is zero-based`)
@@ -57,14 +58,24 @@ export function readLines(filepath: string, endLine?: number, startLine?: number
 		let buffer = ""
 		let lineCount = 0
 		let result = ""
+		let isFirstChunk = true
 
 		// Handle errors
 		input.on("error", reject)
 
 		// Process data chunks directly
 		input.on("data", (chunk) => {
+			// Convert chunk to string
+			let chunkStr = chunk.toString()
+
+			// Strip BOM from the first chunk if present
+			if (isFirstChunk) {
+				chunkStr = stripBom(chunkStr)
+				isFirstChunk = false
+			}
+
 			// Add chunk to buffer
-			buffer += chunk.toString()
+			buffer += chunkStr
 
 			let pos = 0
 			let nextNewline = buffer.indexOf("\n", pos)