Arduino Yun does it have a RTC?
the Yún doesn’t have a real time clock IC on board, so it can’t keep time when is powered off. Instead, it synchronizes with time servers automatically when it powers up and connects to a network using NTP.


(Arduino Blog)

Therefore, the Yun does not have a onboard RTC.


  If there there is no RTC, can I connect a DS1307 to the Atheros AR9331?


Probably not. It comes in a LPCC package, which has the solder joints on the bottom. This needs to be soldered by reflow. The Yun does not have any pins connected directly to that chip. You're probably thinking of the ATmega32u4, the actual Arduino chip. The other one is for a router.

To get the time, you have two options:


Use the time from the time server

A few notes:


  The Yún must be connected to a network to get the correct time. If you used the web-based WiFi interface to configure the Yún for the network, make sure you've selected the proper time zone.

Connect it to a DS1307 (I find this Adafruit tutorial helpful) You'll need only two pins to use this board. One note: there is a way to connect up to 121 I2C devices using these two pins. However, that gets a little more complicated.