diff --git a/src/cargo/core/compiler/mod.rs b/src/cargo/core/compiler/mod.rs
index a9b588c016c..a425a3bda26 100644
--- a/src/cargo/core/compiler/mod.rs
+++ b/src/cargo/core/compiler/mod.rs
@@ -477,6 +477,25 @@ fn rustc(
             paths::set_file_time_no_err(dep_info_loc, timestamp);
         }
 
+        // This mtime shift for .rmeta is a workaround as rustc incremental build
+        // since rust-lang/rust#114669 (1.90.0) skips unnecessary rmeta generation.
+        //
+        // The situation is like this:
+        //
+        // 1. When build script execution's external dependendies
+        //    (rerun-if-changed, rerun-if-env-changed) got updated,
+        //    the execution unit reran and got a newer mtime.
+        // 2. rustc type-checked the associated crate, though with incremental
+        //    compilation, no rmeta regeneration. Its `.rmeta` stays old.
+        // 3. Run `cargo check` again. Cargo found build script execution had
+        //    a new mtime than existing crate rmeta, so re-checking the crate.
+        //    However the check is a no-op (input has no change), so stuck.
+        if mode.is_check() {
+            for output in outputs.iter() {
+                paths::set_file_time_no_err(&output.path, timestamp);
+            }
+        }
+
         Ok(())
     }));
 
diff --git a/tests/testsuite/freshness.rs b/tests/testsuite/freshness.rs
index 0cf673e4f7a..7d626bbb559 100644
--- a/tests/testsuite/freshness.rs
+++ b/tests/testsuite/freshness.rs
@@ -3184,3 +3184,63 @@ fn use_mtime_cache_in_cargo_home() {
 "#]])
         .run();
 }
+
+#[cargo_test]
+fn incremental_build_script_execution_got_new_mtime_and_cargo_check() {
+    // See https://github.com/rust-lang/cargo/issues/16104
+    let p = project()
+        .file("src/lib.rs", "")
+        .file("touch-me", "")
+        .file(
+            "build.rs",
+            r#"fn main() { println!("cargo::rerun-if-changed=touch-me") }"#,
+        )
+        .build();
+
+    p.cargo("check")
+        .env("CARGO_INCREMENTAL", "1")
+        .with_stderr_data(str![[r#"
+[COMPILING] foo v0.0.1 ([ROOT]/foo)
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+
+    if is_coarse_mtime() {
+        sleep_ms(1000);
+    }
+
+    p.change_file("touch-me", "oops");
+
+    // The first one is expected to rerun build script
+    p.cargo("check -v")
+        .env("CARGO_INCREMENTAL", "1")
+        .with_stderr_data(str![[r#"
+[DIRTY] foo v0.0.1 ([ROOT]/foo): the file `touch-me` has changed ([TIME_DIFF_AFTER_LAST_BUILD])
+[COMPILING] foo v0.0.1 ([ROOT]/foo)
+[RUNNING] `[ROOT]/foo/target/debug/build/foo-[HASH]/build-script-build`
+[RUNNING] `rustc --crate-name foo [..]`
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+
+    // subsequent cargo check gets stuck...
+    p.cargo("check -v")
+        .env("CARGO_INCREMENTAL", "1")
+        .with_stderr_data(str![[r#"
+[FRESH] foo v0.0.1 ([ROOT]/foo)
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+
+    p.cargo("check -v")
+        .env("CARGO_INCREMENTAL", "1")
+        .with_stderr_data(str![[r#"
+[FRESH] foo v0.0.1 ([ROOT]/foo)
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+}
diff --git a/tests/testsuite/freshness_checksum.rs b/tests/testsuite/freshness_checksum.rs
index ffc94abb78c..eedc1f43de9 100644
--- a/tests/testsuite/freshness_checksum.rs
+++ b/tests/testsuite/freshness_checksum.rs
@@ -2963,3 +2963,63 @@ fn use_checksum_cache_in_cargo_home() {
 "#]])
         .run();
 }
+
+#[cargo_test(nightly, reason = "requires -Zchecksum-hash-algorithm")]
+fn incremental_build_script_execution_got_new_mtime_and_cargo_check() {
+    // See https://github.com/rust-lang/cargo/issues/16104
+    let p = project()
+        .file("src/lib.rs", "")
+        .file("touch-me", "")
+        .file(
+            "build.rs",
+            r#"fn main() { println!("cargo::rerun-if-changed=touch-me") }"#,
+        )
+        .build();
+
+    p.cargo("check -Zchecksum-freshness")
+        .masquerade_as_nightly_cargo(&["checksum-freshness"])
+        .env("CARGO_INCREMENTAL", "1")
+        .with_stderr_data(str![[r#"
+[COMPILING] foo v0.0.1 ([ROOT]/foo)
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+
+    p.change_file("touch-me", "oops");
+
+    // The first one is expected to rerun build script
+    p.cargo("check -Zchecksum-freshness -v")
+        .masquerade_as_nightly_cargo(&["checksum-freshness"])
+        .env("CARGO_INCREMENTAL", "1")
+        .with_stderr_data(str![[r#"
+[DIRTY] foo v0.0.1 ([ROOT]/foo): the file `touch-me` has changed ([TIME_DIFF_AFTER_LAST_BUILD])
+[COMPILING] foo v0.0.1 ([ROOT]/foo)
+[RUNNING] `[ROOT]/foo/target/debug/build/foo-[HASH]/build-script-build`
+[RUNNING] `rustc --crate-name foo [..]`
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+
+    // subsequent cargo check gets stuck...
+    p.cargo("check -Zchecksum-freshness -v")
+        .masquerade_as_nightly_cargo(&["checksum-freshness"])
+        .env("CARGO_INCREMENTAL", "1")
+        .with_stderr_data(str![[r#"
+[FRESH] foo v0.0.1 ([ROOT]/foo)
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+
+    p.cargo("check -Zchecksum-freshness -v")
+        .masquerade_as_nightly_cargo(&["checksum-freshness"])
+        .env("CARGO_INCREMENTAL", "1")
+        .with_stderr_data(str![[r#"
+[FRESH] foo v0.0.1 ([ROOT]/foo)
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+}