diff --git a/cmake/ConfigureChecks.cmake b/cmake/ConfigureChecks.cmake
index 6b4f0b99f..265a96127 100644
--- a/cmake/ConfigureChecks.cmake
+++ b/cmake/ConfigureChecks.cmake
@@ -19,6 +19,11 @@ if (CMAKE_HOST_SYSTEM_VERSION MATCHES ".*-Microsoft")
   SET(WSL 1)
 endif()
 
+# Detect Cygwin.
+if (CMAKE_SYSTEM_NAME MATCHES "CYGWIN_NT.*")
+  SET(CYGWIN 1)
+endif()
+
 # Set up the config.h file.
 SET(PACKAGE_NAME "fish")
 SET(PACKAGE_TARNAME "fish")
diff --git a/config_cmake.h.in b/config_cmake.h.in
index 47cfcc5e2..162f76de0 100644
--- a/config_cmake.h.in
+++ b/config_cmake.h.in
@@ -4,6 +4,9 @@
 /* Define to 1 if compiled on WSL */
 #cmakedefine WSL 1
 
+/* Define to 1 if complied under Cygwin */
+#cmakedefine CYGWIN 1
+
 /* Define to 1 if you have the `clock_gettime' function. */
 #cmakedefine HAVE_CLOCK_GETTIME 1
 
diff --git a/src/common.h b/src/common.h
index 889036841..dac5d9a6d 100644
--- a/src/common.h
+++ b/src/common.h
@@ -947,6 +947,15 @@ constexpr bool is_windows_subsystem_for_linux() {
 #endif
 }
 
+/// Detect if we are running under Cygwin or Cgywin64
+constexpr bool is_cygwin() {
+#ifdef CYGWIN
+    return true;
+#else
+    return false;
+#endif
+}
+
 extern "C" {
 __attribute__((noinline)) void debug_thread_error(void);
 }
diff --git a/src/proc.cpp b/src/proc.cpp
index 8072a64a7..69494c8dc 100644
--- a/src/proc.cpp
+++ b/src/proc.cpp
@@ -448,9 +448,27 @@ static bool process_mark_finished_children(bool block_on_fg) {
             options &= ~WNOHANG;
         }
 
-        // If the pgid is 0, we need to wait by process because that's invalid.
-        // This happens in firejail for reasons not entirely clear to me.
-        bool wait_by_process = !j->job_chain_is_fully_constructed() || j->pgid == 0;
+        // Child jobs (produced via execution of functions) share job ids with their not-yet-
+        // fully-constructed parent jobs, so we have to wait on these by individual process id
+        // and not by the shared pgroup. End result is the same, but it just makes more calls
+        // to the kernel.
+        bool wait_by_process = !j->job_chain_is_fully_constructed();
+
+        // Firejail can result in jobs with pgroup 0, in which case we cannot wait by
+        // job id. See discussion in #5295.
+        if (j->pgid == 0) {
+            wait_by_process = true;
+        }
+
+        // Cygwin does some voodoo with regards to process management that I do not understand, but
+        // long story short, we cannot reap processes by their pgroup. The way child processes are
+        // launched under Cygwin is... weird, and outwardly they do not appear to retain information
+        // about their parent process when viewed in Task Manager. Waiting on processes by their
+        // pgroup results in never reaping any, so we just wait on them by process id instead.
+        if (is_cygwin()) {
+            wait_by_process = true;
+        }
+
         // When waiting on processes individually in a pipeline, we need to enumerate in reverse
         // order so that the first process we actually wait on (i.e. ~WNOHANG) is the last process
         // in the IO chain, because that's the one that controls the lifetime of the foreground job