In Schneider's sophomore season, he posted a college career-high .929 save percentage and two team records of eight shutouts and 1,088 saves. He posted 242:19 consecutive shutout minutes in the month of January, not allowing a goal for more than 11 periods. His streak was broken on January 27, 2006, in a game against Boston University. His 1.96 GAA was first among goaltenders in conference play, earning him the Hockey East Goaltending Award (his overall GAA including inter-conference play was 2.11). He was named to the Hockey East Second All-Conference Team and was a co-recipient with teammate Chris Collins for both the Hockey East Three Stars Award and Boston College MVP. At the 2006 Beanpot, he received the Eberly Trophy as the tournament's best goaltender with a .924 save percentage. His 24 wins in 39 regular season appearances helped Boston College to a successful regular season. In the playoffs, they failed to defend their Hockey East championship, losing to the Boston University Terriers in the final. Qualifying for the 2006 NCAA Tournament, Boston College met Boston University again in the regional final. Shutting the Terriers out to advance to the Frozen Four, Schneider was named the Northeastern Regional Tournament MVP. Boston College then defeated North Dakota in the semifinal before losing the national championship to the Wisconsin Badgers 2–1.