diff --git a/doc/chrony.conf.adoc b/doc/chrony.conf.adoc
index 6cecc1b..9140c62 100644
--- a/doc/chrony.conf.adoc
+++ b/doc/chrony.conf.adoc
@@ -511,8 +511,10 @@ Note that some PTP clocks cannot be configured to timestamp only assert or
 clear events, and it is necessary to use the *width* option to filter wrong
 PPS samples.
 *pin*=_index_::::
-This option specifies the index of the pin to which is connected the PPS
-signal. The default value is 0.
+This option specifies the index of the pin which should be enabled for the
+PPS timestamping. If the PHC does not have configurable pins (i.e. the channel
+function is fixed), the index needs to be set to -1 to disable the pin
+configuration. The default value is 0.
 *channel*=_index_::::
 This option specifies the index of the channel for the PPS mode. The default
 value is 0.
diff --git a/sys_linux.c b/sys_linux.c
index cc3c931..762bf0a 100644
--- a/sys_linux.c
+++ b/sys_linux.c
@@ -1008,7 +1008,7 @@ SYS_Linux_SetPHCExtTimestamping(int fd, int pin, int channel,
   pin_desc.func = enable ? PTP_PF_EXTTS : PTP_PF_NONE;
   pin_desc.chan = channel;
 
-  if (ioctl(fd, PTP_PIN_SETFUNC, &pin_desc)) {
+  if (pin >= 0 && ioctl(fd, PTP_PIN_SETFUNC, &pin_desc)) {
     DEBUG_LOG("ioctl(%s) failed : %s", "PTP_PIN_SETFUNC", strerror(errno));
     return 0;
   }