In 2009, he came through qualifying to reach the main draw of a Masters Series 1000 tournament for the first time at the Miami Masters. He beat Tommy Haas in the first round, but lost to Dmitry Tursunov in the second round.
In January 2012, Kukushkin became the first player with Kazakh passport to reach the fourth round of the 2012 Australian Open. Later that season, he reached his career-high singles ranking of World No. 49, just after the quarterfinals at Nice and the second round at the 2012 French Open.
By the end of 2012 he suffered from a bad hip injury and had to go under surgery two times. As of August 2013 he was ranked number 430. After recovery he reached the third round of the 2013 US Open, his best performance in the American Grand Slam, starting from the qualifying draw. In September he found a very good form again, winning two Challenger Tournaments in Turkey: Izmir and Istanbul. He then reached his second ATP World Tour final in Moscow, at the Kremlin Cup, beating in the semifinals World No. 22 and defending champion Andreas Seppi.