[1] Shishkin graduated from local football school and at age 15 secured his first professional contract with FC Fakel.

He made his professional debut for Spartak in 2004 when Nevio Scala started fielding a lot of young players.

On 12 September 2006, Shishkin made his European debut after he came in as a substitute in the UEFA Champions League match against Bayern Munich.

[7] On 12 August 2019, he signed with the Russian Football National League club FC Torpedo Moscow.

[12] After a few years' absence from the squad, Shishkin forced his way back into contention following some good performances for Lokomotiv Moscow, and he would play a part in Russia's successful qualifying campaign for Euro 2012.