diff --git a/.gitlab-ci/vkd3d-runner.sh b/.gitlab-ci/vkd3d-runner.sh
index 3f2bfae2a46..175dcd65890 100755
--- a/.gitlab-ci/vkd3d-runner.sh
+++ b/.gitlab-ci/vkd3d-runner.sh
@@ -57,6 +57,35 @@ else
     touch "$EXPECTATIONFILE"
 fi
 
+if [ -f "$INSTALL/$GPU_VERSION-vkd3d-flakes.txt" ]; then
+  mapfile -t flakes < <(grep -vE '^#|^$' "$INSTALL/$GPU_VERSION-vkd3d-flakes.txt")
+else
+  flakes=()
+fi
+
+# Some sanity checks before we start
+mapfile -t flakes_dups < <(
+  [ ${#flakes[@]} -eq 0 ] ||
+  printf '%s\n' "${flakes[@]}" | sort | uniq -d
+)
+if [ ${#flakes_dups[@]} -gt 0 ]; then
+  echo >&2 'Duplicate flakes lines:'
+  printf >&2 '  %s\n' "${flakes_dups[@]}"
+  exit 1
+fi
+
+flakes_in_baseline=()
+for flake in "${flakes[@]}"; do
+  if grep -qF "$flake" "$EXPECTATIONFILE"; then
+    flakes_in_baseline+=("$flake")
+  fi
+done
+if [ ${#flakes_in_baseline[@]} -gt 0 ]; then
+  echo >&2 "Flakes found in $EXPECTATIONFILE:"
+  printf >&2 '  %s\n' "${flakes_in_baseline[@]}"
+  exit 1
+fi
+
 printf "%s\n" "Running vkd3d-proton testsuite..."
 
 if ! /vkd3d-proton-tests/x64/bin/d3d12 &> "$RESULTS/vkd3d-proton-log.txt"; then
@@ -78,11 +107,32 @@ if ! /vkd3d-proton-tests/x64/bin/d3d12 &> "$RESULTS/vkd3d-proton-log.txt"; then
       exit 1
     fi
 
+    # Ignore flakes when comparing
+    STABLERESULTSFILE="$RESULTS/$GPU_VERSION-results-minus-flakes.txt"
+    cp "$RESULTSFILE" "$STABLERESULTSFILE"
+    for flake in "${flakes[@]}"; do
+      grep -vF "$flake" "$STABLERESULTSFILE" > tmp && mv tmp "$STABLERESULTSFILE"
+    done
+
     # Make sure that the failures found in this run match the current expectation
-    if ! diff --color=always -u "$EXPECTATIONFILE" "$RESULTSFILE"; then
+    if ! diff --color=always -u "$EXPECTATIONFILE" "$STABLERESULTSFILE"; then
         error "Changes found, see ${ARTIFACTS_BASE_URL}/results/vkd3d-proton-log.txt"
         exit 1
     fi
+
+    # Print list of flakes seen this time
+    flakes_seen=()
+    for flake in "${flakes[@]}"; do
+      if grep -qF "$flake" "$RESULTSFILE"; then
+        flakes_seen+=("$flake")
+      fi
+    done
+    if [ ${#flakes_seen[@]} -gt 0 ]; then
+      # Keep this string and output format in line with the corresponding
+      # deqp-runner message
+      echo >&2 'Some known flakes found:'
+      printf >&2 '  %s\n' "${flakes_seen[@]}"
+    fi
 fi
 
 exit 0
diff --git a/src/amd/ci/gitlab-ci-inc.yml b/src/amd/ci/gitlab-ci-inc.yml
index 2f3c98c54aa..10a9c86ae09 100644
--- a/src/amd/ci/gitlab-ci-inc.yml
+++ b/src/amd/ci/gitlab-ci-inc.yml
@@ -15,6 +15,7 @@
         - src/amd/ci/$GPU_VERSION-skips.txt
         - src/amd/ci/$PIGLIT_TRACES_FILE
         - src/amd/ci/$GPU_VERSION-vkd3d-fails.txt
+        - src/amd/ci/$GPU_VERSION-vkd3d-flakes.txt
         - src/amd/ci/$GPU_VERSION-vkd3d-skips.txt
         - src/amd/common/**/*
         - src/amd/llvm/**/*