diff --git a/pkgs/by-name/ma/makeBinaryWrapper/make-binary-wrapper.sh b/pkgs/by-name/ma/makeBinaryWrapper/make-binary-wrapper.sh
index 232bc2b5c3cd..595574468ffa 100644
--- a/pkgs/by-name/ma/makeBinaryWrapper/make-binary-wrapper.sh
+++ b/pkgs/by-name/ma/makeBinaryWrapper/make-binary-wrapper.sh
@@ -366,10 +366,10 @@ void set_env_prefix(char *env, char *sep, char *prefix) {
         return;
       }
       unsigned long sep_len = strlen(sep);
-      int n_before = existing_prefix - existing_env;
+      int n_before = existing_prefix - existing_env - sep_len;
       assert_success(asprintf(&val, \"%s%s%.*s%s\", prefix, sep,
                               n_before, existing_env,
-                              existing_prefix + prefix_len + sep_len));
+                              existing_prefix + prefix_len));
     } else {
       assert_success(asprintf(&val, \"%s%s%s\", prefix, sep, existing_env));
     }
diff --git a/pkgs/test/make-binary-wrapper/combination/combination.c b/pkgs/test/make-binary-wrapper/combination/combination.c
index ae90263c45a5..33a003ca6a9a 100644
--- a/pkgs/test/make-binary-wrapper/combination/combination.c
+++ b/pkgs/test/make-binary-wrapper/combination/combination.c
@@ -42,10 +42,10 @@ void set_env_prefix(char *env, char *sep, char *prefix) {
         return;
       }
       unsigned long sep_len = strlen(sep);
-      int n_before = existing_prefix - existing_env;
+      int n_before = existing_prefix - existing_env - sep_len;
       assert_success(asprintf(&val, "%s%s%.*s%s", prefix, sep,
                               n_before, existing_env,
-                              existing_prefix + prefix_len + sep_len));
+                              existing_prefix + prefix_len));
     } else {
       assert_success(asprintf(&val, "%s%s%s", prefix, sep, existing_env));
     }
diff --git a/pkgs/test/make-binary-wrapper/default.nix b/pkgs/test/make-binary-wrapper/default.nix
index 715b28f912e4..7d2e4b1a7cd2 100644
--- a/pkgs/test/make-binary-wrapper/default.nix
+++ b/pkgs/test/make-binary-wrapper/default.nix
@@ -59,6 +59,7 @@ let
       "overlength-strings"
       "prefix"
       "suffix"
+      "prefix-dedup-last"
     ] makeGoldenTest
     // lib.optionalAttrs (!stdenv.hostPlatform.isDarwin) {
       cross =
diff --git a/pkgs/test/make-binary-wrapper/overlength-strings/overlength-strings.c b/pkgs/test/make-binary-wrapper/overlength-strings/overlength-strings.c
index 6a5107d5a4de..0dde8218c3bf 100644
--- a/pkgs/test/make-binary-wrapper/overlength-strings/overlength-strings.c
+++ b/pkgs/test/make-binary-wrapper/overlength-strings/overlength-strings.c
@@ -42,10 +42,10 @@ void set_env_prefix(char *env, char *sep, char *prefix) {
         return;
       }
       unsigned long sep_len = strlen(sep);
-      int n_before = existing_prefix - existing_env;
+      int n_before = existing_prefix - existing_env - sep_len;
       assert_success(asprintf(&val, "%s%s%.*s%s", prefix, sep,
                               n_before, existing_env,
-                              existing_prefix + prefix_len + sep_len));
+                              existing_prefix + prefix_len));
     } else {
       assert_success(asprintf(&val, "%s%s%s", prefix, sep, existing_env));
     }
diff --git a/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.c b/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.c
new file mode 100644
index 000000000000..8f13278a7537
--- /dev/null
+++ b/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.c
@@ -0,0 +1,64 @@
+#define _GNU_SOURCE         /* See feature_test_macros(7) */
+#include <unistd.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <stdio.h>
+#include <string.h>
+
+#define assert_success(e) do { if ((e) < 0) { perror(#e); abort(); } } while (0)
+
+int is_surrounded_by_sep(char *env, char *ptr, unsigned long len, char *sep) {
+  unsigned long sep_len = strlen(sep);
+
+  // Check left side (if not at start)
+  if (env != ptr) {
+    if (ptr - env < sep_len)
+      return 0;
+    if (strncmp(sep, ptr - sep_len, sep_len) != 0) {
+      return 0;
+    }
+  }
+  // Check right side (if not at end)
+  char *end_ptr = ptr + len;
+  if (*end_ptr != '\0') {
+    if (strncmp(sep, ptr + len, sep_len) != 0) {
+      return 0;
+    }
+  }
+
+  return 1;
+}
+
+void set_env_prefix(char *env, char *sep, char *prefix) {
+  char *existing_env = getenv(env);
+  if (existing_env) {
+    char *val;
+
+    char *existing_prefix = strstr(existing_env, prefix);
+    unsigned long prefix_len = strlen(prefix);
+    // If the prefix already exists, remove the original
+    if (existing_prefix && is_surrounded_by_sep(existing_env, existing_prefix, prefix_len, sep)) {
+      if (existing_env == existing_prefix) {
+        return;
+      }
+      unsigned long sep_len = strlen(sep);
+      int n_before = existing_prefix - existing_env - sep_len;
+      assert_success(asprintf(&val, "%s%s%.*s%s", prefix, sep,
+                              n_before, existing_env,
+                              existing_prefix + prefix_len));
+    } else {
+      assert_success(asprintf(&val, "%s%s%s", prefix, sep, existing_env));
+    }
+    assert_success(setenv(env, val, 1));
+    free(val);
+  } else {
+    assert_success(setenv(env, prefix, 1));
+  }
+}
+
+int main(int argc, char **argv) {
+    putenv("PATH=/usr/bin:/usr/local/bin");
+    set_env_prefix("PATH", ":", "/usr/local/bin");
+    argv[0] = "/send/me/flags";
+    return execv("/send/me/flags", argv);
+}
diff --git a/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.cmdline b/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.cmdline
new file mode 100644
index 000000000000..ec2d43b44031
--- /dev/null
+++ b/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.cmdline
@@ -0,0 +1,2 @@
+--set PATH /usr/bin:/usr/local/bin \
+--prefix PATH : /usr/local/bin
diff --git a/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.env b/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.env
new file mode 100644
index 000000000000..6f8f684af379
--- /dev/null
+++ b/pkgs/test/make-binary-wrapper/prefix-dedup-last/prefix-dedup-last.env
@@ -0,0 +1,3 @@
+PATH=/usr/local/bin:/usr/bin
+CWD=SUBST_CWD
+SUBST_ARGV0
diff --git a/pkgs/test/make-binary-wrapper/prefix/prefix.c b/pkgs/test/make-binary-wrapper/prefix/prefix.c
index 205ecd0dcaef..a74cb49861ea 100644
--- a/pkgs/test/make-binary-wrapper/prefix/prefix.c
+++ b/pkgs/test/make-binary-wrapper/prefix/prefix.c
@@ -42,10 +42,10 @@ void set_env_prefix(char *env, char *sep, char *prefix) {
         return;
       }
       unsigned long sep_len = strlen(sep);
-      int n_before = existing_prefix - existing_env;
+      int n_before = existing_prefix - existing_env - sep_len;
       assert_success(asprintf(&val, "%s%s%.*s%s", prefix, sep,
                               n_before, existing_env,
-                              existing_prefix + prefix_len + sep_len));
+                              existing_prefix + prefix_len));
     } else {
       assert_success(asprintf(&val, "%s%s%s", prefix, sep, existing_env));
     }