I recall that he most definitely took part in the Battle of Pride Rock in the first movie. Also, we know that Simba, Nala, and even Timon and Pumbaa were present at the second Battle of the Pridelands near the end of Simba's Pride. However, unless I've forgotten, I don't recall seeing Rafiki there at all.
Obviously, this may be because he knew Mufasa wanted Kovu and Kiara to reunite the Pridelanders and Outlanders, but still, I would think Simba would question his absence, unless Simba sent him specifically to get Kiara (which could also explain why Kiara and Kovu seemed to know where the battle was: Rafiki found them and pointed them to the battle location so that they could intervene in time.)
(Of course, I don't recall Zazu being in this battle much either, if at all, so maybe only lions were ordered to go to the battle and Timon and Pumbaa were made to go as punishment for losing Kiara )