diff --git a/crates/ruff_cli/src/args.rs b/crates/ruff_cli/src/args.rs
index ba2cca1b16558..8c9acaa67e0a8 100644
--- a/crates/ruff_cli/src/args.rs
+++ b/crates/ruff_cli/src/args.rs
@@ -507,6 +507,7 @@ impl CheckCommand {
                 extend_exclude: self.extend_exclude,
                 extend_fixable: self.extend_fixable,
                 extend_ignore: self.extend_ignore,
+                extend_per_file_ignores: self.extend_per_file_ignores,
                 extend_select: self.extend_select,
                 extend_unfixable: self.extend_unfixable,
                 fixable: self.fixable,
@@ -627,6 +628,7 @@ pub struct CliOverrides {
     pub ignore: Option<Vec<RuleSelector>>,
     pub line_length: Option<LineLength>,
     pub per_file_ignores: Option<Vec<PatternPrefixPair>>,
+    pub extend_per_file_ignores: Option<Vec<PatternPrefixPair>>,
     pub preview: Option<PreviewMode>,
     pub respect_gitignore: Option<bool>,
     pub select: Option<Vec<RuleSelector>>,
@@ -657,6 +659,12 @@ impl ConfigurationTransformer for CliOverrides {
         if let Some(extend_exclude) = &self.extend_exclude {
             config.extend_exclude.extend(extend_exclude.clone());
         }
+        if let Some(extend_per_file_ignores) = &self.extend_per_file_ignores {
+            config
+                .lint
+                .extend_per_file_ignores
+                .extend(collect_per_file_ignores(extend_per_file_ignores.clone()));
+        }
         if let Some(fix) = &self.fix {
             config.fix = Some(*fix);
         }
diff --git a/crates/ruff_cli/tests/lint.rs b/crates/ruff_cli/tests/lint.rs
index f6a7a2a99f60f..5602926b95c4f 100644
--- a/crates/ruff_cli/tests/lint.rs
+++ b/crates/ruff_cli/tests/lint.rs
@@ -308,3 +308,87 @@ _ = "---------------------------------------------------------------------------
     "###);
     Ok(())
 }
+
+#[test]
+fn per_file_ignores_stdin() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_toml = tempdir.path().join("ruff.toml");
+    fs::write(
+        &ruff_toml,
+        r#"
+extend-select = ["B", "Q"]
+
+[lint.flake8-quotes]
+inline-quotes = "single"
+"#,
+    )?;
+
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .current_dir(tempdir.path())
+        .arg("check")
+        .args(STDIN_BASE_OPTIONS)
+        .args(["--config", &ruff_toml.file_name().unwrap().to_string_lossy()])
+        .args(["--stdin-filename", "generated.py"])
+        .args(["--per-file-ignores", "generated.py:Q"])
+        .arg("-")
+        .pass_stdin(r#"
+import os
+
+from test import say_hy
+
+if __name__ == "__main__":
+    say_hy("dear Ruff contributor")
+"#), @r###"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    generated.py:2:8: F401 [*] `os` imported but unused
+    Found 1 error.
+    [*] 1 fixable with the `--fix` option.
+
+    ----- stderr -----
+    "###);
+    Ok(())
+}
+
+#[test]
+fn extend_per_file_ignores_stdin() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_toml = tempdir.path().join("ruff.toml");
+    fs::write(
+        &ruff_toml,
+        r#"
+extend-select = ["B", "Q"]
+
+[lint.flake8-quotes]
+inline-quotes = "single"
+"#,
+    )?;
+
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .current_dir(tempdir.path())
+        .arg("check")
+        .args(STDIN_BASE_OPTIONS)
+        .args(["--config", &ruff_toml.file_name().unwrap().to_string_lossy()])
+        .args(["--stdin-filename", "generated.py"])
+        .args(["--extend-per-file-ignores", "generated.py:Q"])
+        .arg("-")
+        .pass_stdin(r#"
+import os
+
+from test import say_hy
+
+if __name__ == "__main__":
+    say_hy("dear Ruff contributor")
+"#), @r###"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    generated.py:2:8: F401 [*] `os` imported but unused
+    Found 1 error.
+    [*] 1 fixable with the `--fix` option.
+
+    ----- stderr -----
+    "###);
+    Ok(())
+}