diff --git a/changelog/13695.contrib.rst b/changelog/13695.contrib.rst
new file mode 100644
index 00000000000..675e1fc96a0
--- /dev/null
+++ b/changelog/13695.contrib.rst
@@ -0,0 +1 @@
+Flush `stdout` and `stderr` in `Pytester.run` to avoid truncated outputs in `test_faulthandler.py::test_timeout` on CI -- by :user:`ogrisel`.
diff --git a/src/_pytest/pytester.py b/src/_pytest/pytester.py
index de4e2c8b136..d5b67abdaee 100644
--- a/src/_pytest/pytester.py
+++ b/src/_pytest/pytester.py
@@ -1422,7 +1422,6 @@ def run(
                 stdin=stdin,
                 stdout=f1,
                 stderr=f2,
-                close_fds=(sys.platform != "win32"),
             )
             if popen.stdin is not None:
                 popen.stdin.close()
@@ -1443,6 +1442,8 @@ def handle_timeout() -> None:
                     ret = popen.wait(timeout)
                 except subprocess.TimeoutExpired:
                     handle_timeout()
+            f1.flush()
+            f2.flush()
 
         with p1.open(encoding="utf8") as f1, p2.open(encoding="utf8") as f2:
             out = f1.read().splitlines()
diff --git a/testing/test_faulthandler.py b/testing/test_faulthandler.py
index d89cb274b78..b308e89adbd 100644
--- a/testing/test_faulthandler.py
+++ b/testing/test_faulthandler.py
@@ -2,6 +2,7 @@
 from __future__ import annotations
 
 import io
+import os
 import sys
 
 from _pytest.pytester import Pytester
@@ -76,7 +77,13 @@ def test_disabled():
     "enabled",
     [
         pytest.param(
-            True, marks=pytest.mark.skip(reason="sometimes crashes on CI (#7022)")
+            True,
+            marks=pytest.mark.skipif(
+                "CI" in os.environ
+                and sys.platform == "linux"
+                and sys.version_info >= (3, 14),
+                reason="sometimes crashes on CI because of truncated outputs (#7022)",
+            ),
         ),
         False,
     ],
diff --git a/testing/test_terminal.py b/testing/test_terminal.py
index 8c50311e9aa..2a3f4446a11 100644
--- a/testing/test_terminal.py
+++ b/testing/test_terminal.py
@@ -2250,8 +2250,8 @@ def test_times_multiline(
         output.stdout.re_match_lines(
             [
                 r"test_bar.py ...................",
-                r"........... \s+ \d{1,3}[\.[a-z\ ]{1,2}\d{0,3}\w{1,2}$",
-                r"test_foo.py \.{5} \s+ \d{1,3}[\.[a-z\ ]{1,2}\d{0,3}\w{1,2}$",
+                r"........... \s+ \d{1,4}[\.[a-z\ ]{1,2}\d{0,3}\w{1,2}$",
+                r"test_foo.py \.{5} \s+ \d{1,4}[\.[a-z\ ]{1,2}\d{0,3}\w{1,2}$",
             ],
             consecutive=True,
         )