diff --git a/repos/spack_repo/builtin/packages/kallisto/package.py b/repos/spack_repo/builtin/packages/kallisto/package.py
index f671ea91d97..8ac58643530 100644
--- a/repos/spack_repo/builtin/packages/kallisto/package.py
+++ b/repos/spack_repo/builtin/packages/kallisto/package.py
@@ -46,6 +46,13 @@ class Kallisto(CMakePackage):
     patch("limits.patch", when="@:0.46")
     patch("htslib_configure.patch", when="@0.44.0:0.48.0^autoconf@2.70:")
 
+    # https://github.com/pachterlab/kallisto/pull/506
+    patch(
+        "https://github.com/pachterlab/kallisto/commit/a5caefb.patch?full_index=1",
+        sha256="a7002ce51d4dfeab8bce3e1d696ad034328b38e6d794de0c1400d07fb77e018a",
+        when="@0.50.1:",
+    )
+
     @run_before("cmake")
     def autoreconf(self):
         # Versions of autoconf greater than 2.69 need config.guess and