Second period goals by Alex Esposito and Ross Colton, his team-leading 13th of the season, helped Vermont overcome an early deficit to earn the 2-1 victory.
Stefanos Lekkas made 23 saves to earn his sixth victory of the season.
Brett Seney scored the only goal of the game for Merrimack on the Warriors only power play at 9:34 of the first.
Vermont, combined with their 6-3 victory over UMass Lowell on Saturday, has won back-to-back games for the first time this season.