diff --git a/Cargo.lock b/Cargo.lock
index 95db78e..b6f7d95 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1459,6 +1459,12 @@ version = "4.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d211803b9b6b570f68772237e415a029d5a50c65d382910b879fb19d3271f94d"
 
+[[package]]
+name = "pathdiff"
+version = "0.2.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "df94ce210e5bc13cb6651479fa48d14f601d9858cfe0467f43ae157023b938d3"
+
 [[package]]
 name = "pep440_rs"
 version = "0.7.3"
@@ -1594,6 +1600,7 @@ dependencies = [
  "log",
  "logging_timer",
  "pex",
+ "platform",
  "regex",
  "venv",
 ]
@@ -1630,6 +1637,7 @@ dependencies = [
  "fs-err",
  "is_executable",
  "nix",
+ "pathdiff",
 ]
 
 [[package]]
diff --git a/Cargo.toml b/Cargo.toml
index 62fcf20..346a70d 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -118,6 +118,7 @@ log = "0.4"
 logging_timer = "1.1"
 nix = {  version = "0.31", features = ["fs"] }
 owo-colors = "4.3"
+pathdiff = "0.2"
 pep440_rs = "0.7"
 pep508_rs = "0.9"
 python-pkginfo = "0.6"
diff --git a/crates/pexrs/Cargo.toml b/crates/pexrs/Cargo.toml
index 8251323..0063745 100644
--- a/crates/pexrs/Cargo.toml
+++ b/crates/pexrs/Cargo.toml
@@ -14,5 +14,6 @@ itertools = { workspace = true }
 log = { workspace = true }
 logging_timer = { workspace = true }
 pex = { path = "../pex" }
+platform = { path = "../platform" }
 regex = { workspace = true }
 venv = { path = "../venv" }
\ No newline at end of file
diff --git a/crates/pexrs/src/lib.rs b/crates/pexrs/src/lib.rs
index b265b9a..6a63a5c 100644
--- a/crates/pexrs/src/lib.rs
+++ b/crates/pexrs/src/lib.rs
@@ -112,9 +112,10 @@ fn prepare_venv<'a>(
         #[cfg(unix)]
         if let Some(sh_boot_seed_dir) = sh_boot_seed_dir {
             fs::create_dir_all(&sh_boot_seed_dir)?;
-            std::os::unix::fs::symlink(
+            platform::unix::symlink(
                 venv_dir.join("pex"),
                 sh_boot_seed_dir.join(venv_interpreter.most_specific_exe_name()),
+                true,
             )?;
         }
         Virtualenv::enclosing(venv_interpreter)
diff --git a/crates/platform/Cargo.toml b/crates/platform/Cargo.toml
index de489ce..39374cd 100644
--- a/crates/platform/Cargo.toml
+++ b/crates/platform/Cargo.toml
@@ -8,6 +8,7 @@ edition = "2024"
 [dependencies]
 anyhow = { workspace = true }
 fs-err = { workspace = true }
+pathdiff = { workspace = true }
 
 # N.B.: Although is_executable is cross-platform, we only use it for Windows. The nix unistd access
 # function is more robust that the check is_executable does on unix.
diff --git a/crates/platform/src/lib.rs b/crates/platform/src/lib.rs
index 07cecfb..3ddbf50 100644
--- a/crates/platform/src/lib.rs
+++ b/crates/platform/src/lib.rs
@@ -2,7 +2,7 @@
 // SPDX-License-Identifier: Apache-2.0
 
 #[cfg(unix)]
-mod unix;
+pub mod unix;
 
 #[cfg(windows)]
 mod windows;
diff --git a/crates/platform/src/unix.rs b/crates/platform/src/unix.rs
index 6c9e87b..79d060d 100644
--- a/crates/platform/src/unix.rs
+++ b/crates/platform/src/unix.rs
@@ -1,9 +1,10 @@
 // Copyright 2026 Pex project contributors.
 // SPDX-License-Identifier: Apache-2.0
 
+use std::borrow::Cow;
 use std::fs::File;
 use std::os::unix::ffi::OsStrExt;
-use std::os::unix::fs::{PermissionsExt, symlink};
+use std::os::unix::fs::PermissionsExt;
 use std::path::Path;
 
 use anyhow::{anyhow, bail};
@@ -11,8 +12,24 @@ use nix::errno::Errno;
 use nix::unistd;
 use nix::unistd::AccessFlags;
 
-pub fn link_or_copy(src: impl AsRef<Path>, dst: impl AsRef<Path>) -> anyhow::Result<()> {
-    symlink(src, dst).map_err(anyhow::Error::new)
+pub fn link_or_copy(
+    src: impl AsRef<Path>,
+    dst: impl AsRef<Path>,
+    relative: bool,
+) -> anyhow::Result<()> {
+    symlink(src, dst, relative)
+}
+
+pub fn symlink(src: impl AsRef<Path>, dst: impl AsRef<Path>, relative: bool) -> anyhow::Result<()> {
+    let src = if relative
+        && let Some(rel_base) = dst.as_ref().parent()
+        && let Some(rel_path) = pathdiff::diff_paths(src.as_ref(), rel_base)
+    {
+        Cow::Owned(rel_path)
+    } else {
+        Cow::Borrowed(src.as_ref())
+    };
+    std::os::unix::fs::symlink(src, dst).map_err(anyhow::Error::new)
 }
 
 pub fn is_executable(path: impl AsRef<Path>) -> anyhow::Result<bool> {
diff --git a/crates/platform/src/windows.rs b/crates/platform/src/windows.rs
index 4f896af..769e608 100644
--- a/crates/platform/src/windows.rs
+++ b/crates/platform/src/windows.rs
@@ -7,7 +7,11 @@ use std::path::Path;
 use fs_err as fs;
 use is_executable::IsExecutable;
 
-pub fn link_or_copy(src: impl AsRef<Path>, dst: impl AsRef<Path>) -> anyhow::Result<()> {
+pub fn link_or_copy(
+    src: impl AsRef<Path>,
+    dst: impl AsRef<Path>,
+    _relative: bool,
+) -> anyhow::Result<()> {
     fs::hard_link(&src, &dst)
         .or_else(|_| fs::copy(src, dst).map(|_| ()))
         .map_err(anyhow::Error::new)
diff --git a/crates/venv/src/venv_pex.rs b/crates/venv/src/venv_pex.rs
index daf9a57..2a22918 100644
--- a/crates/venv/src/venv_pex.rs
+++ b/crates/venv/src/venv_pex.rs
@@ -263,7 +263,7 @@ if __name__ == "__main__":
         )
     )?;
     mark_executable(main_py_fp.file_mut())?;
-    link_or_copy(&main_py, venv.prefix().join("pex"))
+    link_or_copy(&main_py, venv.prefix().join("pex"), true)
 }
 
 fn write_repl<'a>(
diff --git a/crates/venv/src/virtualenv.rs b/crates/venv/src/virtualenv.rs
index da02ca2..68b15f6 100644
--- a/crates/venv/src/virtualenv.rs
+++ b/crates/venv/src/virtualenv.rs
@@ -129,7 +129,11 @@ fn create_pep_405_venv<'a>(
     )?;
     let scripts_dir = path.join(SCRIPTS_DIR);
     fs::create_dir_all(&scripts_dir)?;
-    link_or_copy(&base_interpreter.realpath, scripts_dir.join(PYTHON_EXE))?;
+    link_or_copy(
+        &base_interpreter.realpath,
+        scripts_dir.join(PYTHON_EXE),
+        false,
+    )?;
     let site_packages_relpath = site_packages_relpath(&base_interpreter);
     fs::create_dir_all(path.join(site_packages_relpath.as_ref()))?;
     Ok(site_packages_relpath)