Shishkin graduated from local football school and at age 15 secured his first professional contract with FC Fakel. After some time with Fakel he moved to Spartak Moscow. He made his professional debut for Spartak in 2004 when Nevio Scala started fielding a lot of young players. His Russian Premier League debut was on 7 July 2004 in a game against FC Kuban Krasnodar. Roman eventually lost his position in the first team. In 2006 when Fedotov was appointed as a manager, Shishkin became a first team regular. Shishkin played as a right fullback. 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. At the end of 2006 UEFA named Shishkin among Europe's eight most prospective footballers and described him as having a good shot from distance and being useful from set-pieces In 2009, FC Spartak Moscow sent Shiskin on loan to FC Krylia Sovetov Samara. On 6 July 2010, Shishkin signed with Lokomotiv Moscow. His attitude and performances for the club were rewarded in 2013 when he was named vice-captain by manager Slaven Bilić. On 28 January 2017, he joined FC Krasnodar on loan until the end of the 2016–17 season. On 3 July 2017, he returned to FC Krasnodar, signing a 3-year contract as a free agent upon the expiration of his Lokomotiv contract. On 13 January 2019, he returned to PFC Krylia Sovetov Samara on loan until the end of the 2018–19 season. On 11 July 2019, Shishkin left Krasnodar by mutual consent. On 12 August 2019, he signed with the Russian Football National League club FC Torpedo Moscow. His Torpedo contract was terminated by mutual consent on 17 February 2020. On 19 February 2020 he was registered as a player of FC Spartak-2 Moscow.
International
Shiskin was invited by Guus Hiddink to participate in the national team training sessions. His debut for the national team took place on 24 March 2007 as he played the whole match during Russia's 2–0 victory over Estonia. 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. He was named in Dick Advocaat's provisional squad for the tournament itself, but had to withdraw due to a stomach ailment. Shishkin did not appear for the national team again until late 2015, when he featured in friendlies against Portugal and Croatia. He was then included by Leonid Slutsky in the Russian squad for Euro 2016.
