Nikishyn was excluded from the national team in the 2004–05 season, but he was reinstated the next season. He achieved his first World Cup podium with a bronze medal in the Doha Grand Prix. At the 2006 World Championships in Turin he was eliminated in the qualifications phase of the individual event. In the team event Nikishyn, Dmytro Karyuchenko, Maksym Khvorost and Dmytro Chumak were defeated in the semi-finals, then overcame Hungary to earn Ukraine's first world medal in team épée.