diff --git a/pkgs/tools/misc/hdf5/default.nix b/pkgs/tools/misc/hdf5/default.nix
index 43c156de419e..5671e73c85f8 100644
--- a/pkgs/tools/misc/hdf5/default.nix
+++ b/pkgs/tools/misc/hdf5/default.nix
@@ -67,6 +67,13 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./bin-mv.patch
+
+    # Avoid non-determinism in autoconf build system:
+    # - build time
+    # - build user
+    # - uname -a (kernel version)
+    # Can be dropped once/if we switch to cmake.
+    ./hdf5-more-determinism.patch
   ];
 
   postInstall = ''
diff --git a/pkgs/tools/misc/hdf5/hdf5-more-determinism.patch b/pkgs/tools/misc/hdf5/hdf5-more-determinism.patch
new file mode 100644
index 000000000000..9a9bfe24af7b
--- /dev/null
+++ b/pkgs/tools/misc/hdf5/hdf5-more-determinism.patch
@@ -0,0 +1,15 @@
+diff --git a/src/libhdf5.settings.in b/src/libhdf5.settings.in
+index a4d4af6..70f1909 100644
+--- a/src/libhdf5.settings.in
++++ b/src/libhdf5.settings.in
+@@ -4,10 +4,7 @@
+ General Information:
+ -------------------
+                    HDF5 Version: @H5_VERSION@
+-                  Configured on: @CONFIG_DATE@
+-                  Configured by: @CONFIG_USER@
+                     Host system: @host_cpu@-@host_vendor@-@host_os@
+-              Uname information: @UNAME_INFO@
+                        Byte sex: @BYTESEX@
+              Installation point: @prefix@
+