diff --git a/crates/uv/src/commands/pip_compile.rs b/crates/uv/src/commands/pip_compile.rs
index 602fe2900947..0532663ba7bd 100644
--- a/crates/uv/src/commands/pip_compile.rs
+++ b/crates/uv/src/commands/pip_compile.rs
@@ -352,14 +352,7 @@ pub(crate) async fn pip_compile(
         writeln!(
             writer,
             "{}",
-            format!(
-                "#    uv {}",
-                env::args_os()
-                    .skip(1)
-                    .map(|arg| arg.normalized_display().to_string())
-                    .join(" ")
-            )
-            .green()
+            format!("#    {}", cmd(include_index_url)).green()
         )?;
     }
 
@@ -398,13 +391,43 @@ pub(crate) async fn pip_compile(
             &resolution,
             generate_hashes,
             include_annotations,
-            annotation_style
+            annotation_style,
         )
     )?;
 
     Ok(ExitStatus::Success)
 }
 
+/// Format the `uv` command used to generate the output file.
+fn cmd(include_index_url: bool) -> String {
+    let args = env::args_os()
+        .skip(1)
+        .map(|arg| arg.normalized_display().to_string())
+        .scan(None, move |skip_next, arg| {
+            if let Some(true) = skip_next {
+                // Reset state; skip this iteration.
+                *skip_next = None;
+                Some(None)
+            } else if !include_index_url
+                && (arg.starts_with("--extra-index-url=") || arg.starts_with("--index-url="))
+            {
+                // Reset state; skip this iteration.
+                *skip_next = None;
+                Some(None)
+            } else if !include_index_url && (arg == "--extra-index-url" || arg == "--index-url") {
+                // Mark the next item as (to be) skipped.
+                *skip_next = Some(true);
+                Some(None)
+            } else {
+                // Return the argument.
+                Some(Some(arg))
+            }
+        })
+        .flatten()
+        .join(" ");
+    format!("uv {args}")
+}
+
 /// Whether to allow package upgrades.
 #[derive(Debug)]
 pub(crate) enum Upgrade {
diff --git a/crates/uv/tests/pip_compile.rs b/crates/uv/tests/pip_compile.rs
index 2857465e06b0..7f4a7531b802 100644
--- a/crates/uv/tests/pip_compile.rs
+++ b/crates/uv/tests/pip_compile.rs
@@ -650,9 +650,9 @@ fn compile_python_37() -> Result<()> {
             "",
         ),
     ]
-    .into_iter()
-    .chain(INSTA_FILTERS.to_vec())
-    .collect();
+        .into_iter()
+        .chain(INSTA_FILTERS.to_vec())
+        .collect();
 
     uv_snapshot!(filters, context.compile()
             .arg("requirements.in")
@@ -2608,7 +2608,7 @@ fn compile_html() -> Result<()> {
     exit_code: 0
     ----- stdout -----
     # This file was autogenerated by uv via the following command:
-    #    uv pip compile requirements.in --cache-dir [CACHE_DIR] --index-url https://download.pytorch.org/whl
+    #    uv pip compile requirements.in --cache-dir [CACHE_DIR]
     jinja2==3.1.2
     markupsafe==2.1.3
         # via jinja2
@@ -2636,7 +2636,7 @@ fn trailing_slash() -> Result<()> {
     exit_code: 0
     ----- stdout -----
     # This file was autogenerated by uv via the following command:
-    #    uv pip compile --cache-dir [CACHE_DIR] --exclude-newer 2023-11-18T12:00:00Z requirements.in --index-url https://test.pypi.org/simple
+    #    uv pip compile --cache-dir [CACHE_DIR] --exclude-newer 2023-11-18T12:00:00Z requirements.in
     jinja2==3.1.2
     markupsafe==2.1.3
         # via jinja2
@@ -2654,7 +2654,7 @@ fn trailing_slash() -> Result<()> {
     exit_code: 0
     ----- stdout -----
     # This file was autogenerated by uv via the following command:
-    #    uv pip compile --cache-dir [CACHE_DIR] --exclude-newer 2023-11-18T12:00:00Z requirements.in --index-url https://test.pypi.org/simple/
+    #    uv pip compile --cache-dir [CACHE_DIR] --exclude-newer 2023-11-18T12:00:00Z requirements.in
     jinja2==3.1.2
     markupsafe==2.1.3
         # via jinja2
@@ -3393,6 +3393,7 @@ fn resolver_legacy() -> Result<()> {
 }
 
 /// Emit the `--index-url` and `--extra-index-url` locations.
+/// Also, preserve the `--index-url` and `--extra-index-url` flags in the command in the header.
 #[test]
 fn emit_index_urls() -> Result<()> {
     let context = TestContext::new("3.12");
@@ -3499,7 +3500,8 @@ fn no_index_requirements_txt() -> Result<()> {
 }
 
 /// Prefer the `--index-url` from the command line over the `--index-url` in a `requirements.txt`
-/// file.
+/// file. Also, `--index-url` and `--extra-index-url` should not be presented in the output
+/// unless we specify `--emit-index-url`.
 #[test]
 fn index_url_requirements_txt() -> Result<()> {
     let context = TestContext::new("3.12");
@@ -3514,7 +3516,7 @@ fn index_url_requirements_txt() -> Result<()> {
     exit_code: 0
     ----- stdout -----
     # This file was autogenerated by uv via the following command:
-    #    uv pip compile --cache-dir [CACHE_DIR] --exclude-newer 2023-11-18T12:00:00Z requirements.in --index-url https://pypi.org/simple
+    #    uv pip compile --cache-dir [CACHE_DIR] --exclude-newer 2023-11-18T12:00:00Z requirements.in
     tqdm==4.66.1
 
     ----- stderr -----
@@ -3905,7 +3907,7 @@ fn index_url_from_command_line() -> Result<()> {
     exit_code: 0
     ----- stdout -----
     # This file was autogenerated by uv via the following command:
-    #    uv pip compile --cache-dir [CACHE_DIR] --exclude-newer 2023-11-18T12:00:00Z requirements.in --index-url https://pypi.org/simple
+    #    uv pip compile --cache-dir [CACHE_DIR] --exclude-newer 2023-11-18T12:00:00Z requirements.in
     anyio==3.7.1
     idna==3.4
         # via anyio
diff --git a/crates/uv/tests/pip_compile_scenarios.rs b/crates/uv/tests/pip_compile_scenarios.rs
index 865ce378e9e0..8fb0548b940e 100644
--- a/crates/uv/tests/pip_compile_scenarios.rs
+++ b/crates/uv/tests/pip_compile_scenarios.rs
@@ -83,7 +83,7 @@ fn requires_incompatible_python_version_compatible_override() -> Result<()> {
                  exit_code: 0
                  ----- stdout -----
                  # This file was autogenerated by uv via the following command:
-                 #    uv pip compile requirements.in --index-url https://test.pypi.org/simple --find-links https://raw.githubusercontent.com/zanieb/packse/de0bab473eeaa4445db5a8febd732c655fad3d52/vendor/links.html --cache-dir [CACHE_DIR] --python-version=3.11
+                 #    uv pip compile requirements.in --find-links https://raw.githubusercontent.com/zanieb/packse/de0bab473eeaa4445db5a8febd732c655fad3d52/vendor/links.html --cache-dir [CACHE_DIR] --python-version=3.11
                  albatross==1.0.0
 
                  ----- stderr -----
@@ -244,7 +244,7 @@ fn requires_incompatible_python_version_compatible_override_no_wheels_available_
                  exit_code: 0
                  ----- stdout -----
                  # This file was autogenerated by uv via the following command:
-                 #    uv pip compile requirements.in --index-url https://test.pypi.org/simple --find-links https://raw.githubusercontent.com/zanieb/packse/de0bab473eeaa4445db5a8febd732c655fad3d52/vendor/links.html --cache-dir [CACHE_DIR] --python-version=3.11
+                 #    uv pip compile requirements.in --find-links https://raw.githubusercontent.com/zanieb/packse/de0bab473eeaa4445db5a8febd732c655fad3d52/vendor/links.html --cache-dir [CACHE_DIR] --python-version=3.11
                  albatross==1.0.0
 
                  ----- stderr -----
@@ -464,7 +464,7 @@ fn requires_python_patch_version_override_patch_compatible() -> Result<()> {
                  exit_code: 0
                  ----- stdout -----
                  # This file was autogenerated by uv via the following command:
-                 #    uv pip compile requirements.in --index-url https://test.pypi.org/simple --find-links https://raw.githubusercontent.com/zanieb/packse/de0bab473eeaa4445db5a8febd732c655fad3d52/vendor/links.html --cache-dir [CACHE_DIR] --python-version=3.8.0
+                 #    uv pip compile requirements.in --find-links https://raw.githubusercontent.com/zanieb/packse/de0bab473eeaa4445db5a8febd732c655fad3d52/vendor/links.html --cache-dir [CACHE_DIR] --python-version=3.8.0
                  albatross==1.0.0
 
                  ----- stderr -----