diff --git a/doc/hooks/cmake.section.md b/doc/hooks/cmake.section.md
index 5bcc3c980fc5..4aecc8440c64 100644
--- a/doc/hooks/cmake.section.md
+++ b/doc/hooks/cmake.section.md
@@ -33,3 +33,21 @@ The default value is `build`.
 #### `dontUseCmakeConfigure` {#dont-use-cmake-configure}
 
 When set to true, don't use the predefined `cmakeConfigurePhase`.
+
+## Controlling CTest invocation {#cmake-ctest}
+
+By default tests are run by make in [`checkPhase`](#ssec-check-phase) or by [ninja](#ninja) if `ninja` is
+available in `nativeBuildInputs`. Makefile and Ninja generators produce the `test` target, which invokes `ctest` under the hood.
+This makes passing additional arguments to `ctest` difficult, so it's possible to invoke it directly in `checkPhase`
+by adding `ctestCheckHook` to `nativeCheckInputs`.
+
+### CTest Variables {#cmake-ctest-variables}
+
+#### `disabledTests` {#cmake-ctest-disabled-tests}
+
+Allows to disable running a list of tests. Note that regular expressions are not supported by `disabledTests`, but
+it can be combined with `--exclude-regex` option.
+
+#### `ctestFlags` {#cmake-ctest-flags}
+
+Additional options passed to `ctest` together with `checkFlags`.
diff --git a/doc/redirects.json b/doc/redirects.json
index 77c2ffba7b1e..3d4b4a4c084e 100644
--- a/doc/redirects.json
+++ b/doc/redirects.json
@@ -5,6 +5,18 @@
   "chap-release-notes": [
     "release-notes.html#chap-release-notes"
   ],
+  "cmake-ctest": [
+    "index.html#cmake-ctest"
+  ],
+  "cmake-ctest-disabled-tests": [
+    "index.html#cmake-ctest-disabled-tests"
+  ],
+  "cmake-ctest-flags": [
+    "index.html#cmake-ctest-flags"
+  ],
+  "cmake-ctest-variables": [
+    "index.html#cmake-ctest-variables"
+  ],
   "ex-build-helpers-extendMkDerivation": [
     "index.html#ex-build-helpers-extendMkDerivation"
   ],
diff --git a/pkgs/applications/audio/zynaddsubfx/default.nix b/pkgs/applications/audio/zynaddsubfx/default.nix
index fdcfc0a8005e..f6ac1294fc2a 100644
--- a/pkgs/applications/audio/zynaddsubfx/default.nix
+++ b/pkgs/applications/audio/zynaddsubfx/default.nix
@@ -45,6 +45,7 @@
   # Test dependencies
   cxxtest,
   ruby,
+  ctestCheckHook,
 }:
 
 assert builtins.any (g: guiModule == g) [
@@ -151,28 +152,19 @@ stdenv.mkDerivation rec {
   nativeCheckInputs = [
     cxxtest
     ruby
+    ctestCheckHook
   ];
 
-  # TODO: Update cmake hook to make it simpler to selectively disable cmake tests: #113829
-  checkPhase =
-    let
-      disabledTests =
-        # PortChecker is non-deterministic. It's fixed in the master
-        # branch, but backporting would require an update to rtosc, so
-        # we'll just disable it until the next release.
-        [ "PortChecker" ]
-
-        # Tests fail on aarch64
-        ++ lib.optionals stdenv.hostPlatform.isAarch64 [
-          "MessageTest"
-          "UnisonTest"
-        ];
-    in
-    ''
-      runHook preCheck
-      ctest --output-on-failure -E '^${lib.concatStringsSep "|" disabledTests}$'
-      runHook postCheck
-    '';
+  disabledTests =
+    # PortChecker is non-deterministic. It's fixed in the master
+    # branch, but backporting would require an update to rtosc, so
+    # we'll just disable it until the next release.
+    [ "PortChecker" ]
+    # Tests fail on aarch64
+    ++ lib.optionals stdenv.hostPlatform.isAarch64 [
+      "MessageTest"
+      "UnisonTest"
+    ];
 
   # Use Zyn-Fusion logo for zest build
   # An SVG version of the logo isn't hosted anywhere we can fetch, I
diff --git a/pkgs/by-name/ct/ctestCheckHook/ctest-check-hook.sh b/pkgs/by-name/ct/ctestCheckHook/ctest-check-hook.sh
new file mode 100644
index 000000000000..65d39923f967
--- /dev/null
+++ b/pkgs/by-name/ct/ctestCheckHook/ctest-check-hook.sh
@@ -0,0 +1,44 @@
+# shellcheck shell=bash disable=SC2154
+
+ctestCheckHook() {
+    echo "Executing ctestCheckHook"
+
+    runHook preCheck
+
+    local buildCores=1
+
+    if [ "${enableParallelChecking-1}" ]; then
+        buildCores="$NIX_BUILD_CORES"
+    fi
+
+    local flagsArray=(
+        "-j$buildCores"
+        # This is enabled by the cmakeConfigurePhase by exporting
+        # CTEST_OUTPUT_ON_FAILURE, but it makes sense it enable it globally here
+        # as well.
+        "--output-on-failure"
+    )
+
+    local disabledTestsArray=()
+    concatTo disabledTestsArray disabledTests
+
+    if [ ${#disabledTestsArray[@]} -ne 0 ]; then
+        local ctestExcludedTestsFile=$NIX_BUILD_TOP/.ctest-excluded-tests
+        disabledTestsString="$(concatStringsSep "\n" disabledTestsArray)"
+        echo -e "$disabledTestsString" >"$ctestExcludedTestsFile"
+        flagsArray+=("--exclude-from-file" "$ctestExcludedTestsFile")
+    fi
+
+    concatTo flagsArray ctestFlags checkFlags checkFlagsArray
+
+    echoCmd 'ctest flags' "${flagsArray[@]}"
+    ctest "${flagsArray[@]}"
+
+    echo "Finished ctestCheckHook"
+
+    runHook postCheck
+}
+
+if [ -z "${dontUseCTestCheck-}" ] && [ -z "${checkPhase-}" ]; then
+    checkPhase=ctestCheckHook
+fi
diff --git a/pkgs/by-name/ct/ctestCheckHook/package.nix b/pkgs/by-name/ct/ctestCheckHook/package.nix
new file mode 100644
index 000000000000..631b2ba8b86a
--- /dev/null
+++ b/pkgs/by-name/ct/ctestCheckHook/package.nix
@@ -0,0 +1,9 @@
+{
+  makeSetupHook,
+  cmake,
+}:
+
+makeSetupHook {
+  name = "ctestCheckHook";
+  propagatedBuildInputs = [ cmake ];
+} ./ctest-check-hook.sh
diff --git a/pkgs/by-name/gi/gifticlib/package.nix b/pkgs/by-name/gi/gifticlib/package.nix
index d20a554c318b..acd9dabbab9e 100644
--- a/pkgs/by-name/gi/gifticlib/package.nix
+++ b/pkgs/by-name/gi/gifticlib/package.nix
@@ -6,6 +6,7 @@
   expat,
   nifticlib,
   zlib,
+  ctestCheckHook,
 }:
 
 stdenv.mkDerivation {
@@ -33,11 +34,11 @@ stdenv.mkDerivation {
 
   # without the test data, this is only a few basic tests
   doCheck = !stdenv.hostPlatform.isDarwin;
-  checkPhase = ''
-    runHook preCheck
-    ctest -LE 'NEEDS_DATA'
-    runHook postCheck
-  '';
+  nativeCheckInputs = [ ctestCheckHook ];
+  checkFlags = [
+    "-LE"
+    "NEEDS_DATA"
+  ];
 
   meta = with lib; {
     homepage = "https://www.nitrc.org/projects/gifti";
diff --git a/pkgs/by-name/pd/pdal/package.nix b/pkgs/by-name/pd/pdal/package.nix
index f09062a3c5bc..8fae42c069e9 100644
--- a/pkgs/by-name/pd/pdal/package.nix
+++ b/pkgs/by-name/pd/pdal/package.nix
@@ -2,6 +2,7 @@
   lib,
   stdenv,
   callPackage,
+  ctestCheckHook,
   fetchFromGitHub,
   testers,
 
@@ -92,6 +93,9 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   doCheck = true;
+  # tests are flaky and they seem to fail less often when they don't run in
+  # parallel
+  enableParallelChecking = false;
 
   disabledTests = [
     # Tests failing due to TileDB library implementation, disabled also
@@ -116,16 +120,9 @@ stdenv.mkDerivation (finalAttrs: {
 
   nativeCheckInputs = [
     gdal # gdalinfo
+    ctestCheckHook
   ];
 
-  checkPhase = ''
-    runHook preCheck
-    # tests are flaky and they seem to fail less often when they don't run in
-    # parallel
-    ctest -j 1 --output-on-failure -E '^${lib.concatStringsSep "|" finalAttrs.disabledTests}$'
-    runHook postCheck
-  '';
-
   postInstall = ''
     patchShebangs --update --build $out/bin/pdal-config
   '';