In this example, pin #12 was selected (GPIOX.BIT10), GPIO 238, to be the PPS input. You can use any other GPIO here.
Check the pin number and export number to use on gpio_pin

Thanks to dan_d for providing kernel patches + forum info. Forum Thread

Enabling GPIO PPS Client
sudo -s
apt-get install pps-tools
echo pps-gpio > /etc/modules-load.d/pps-gpio.conf
echo options pps-gpio gpio_pin=238 > /etc/modprobe.d/pps-gpio.conf
modprobe pps-gpio
Testing GPIO PPS Client

Start feeding the signal to selected pin #12. Remember that the logic voltage is 3.3V.

sudo -s
ppstest /dev/pps0

Will output something like:

source 0 - assert 1439248167.494093618, sequence: 552 - clear  0.000000000, sequence: 0
source 0 - assert 1439248167.494140618, sequence: 553 - clear  0.000000000, sequence: 0

Note this example will only run on kernel 3.14.65-70 or higher.