Both films landed 10 nominations each, including best animated feature.
Despicable Me 2 and The Croods also compete for the event’s top prize, as do Japanese titles The Wind Rises and A Letter to Momo and the French animation Ernest and Celestine.
The awards will be handed out at a Los Angeles ceremony on February 1st, 2014.
The evening will see director Steven Spielberg recognized for his career contribution to the art of animation.
Frozen‘s other nominations include nods for character animation and design, writing and music in an animated feature.
The film is an adaptation of Hans Christian Andersen’s The Snow Queen.
Monsters University, a prequel to 2001’s Monsters, Inc, is also up for best animated effects, production design and storyboarding.
Despicable Me 2 scored nine nominations in the main feature film categories, with three of its stars – Steve Carell, Kristen Wiig and Pierre Coffin – recognized for voice acting.
Billy Crystal was also nominated for Monsters University, as were Paul Giamatti for Turbo, Terry Crews for Cloudy with a Chance of Meatballs 2 and Josh Gad for Frozen.
The Croods, about a family of cavemen fighting for survival, also received nine nominations.
Frozen and Ernest and Celestine were the only films to be nominated in the best feature, directing and writing categories.
Disney picked up 31 nominations across the 30 categories, which encompass film, TV games and commercials.
DreamWorks followed with 19 nominations, one more than the number Pixar recorded.
The Annie Awards usually indicate which titles will be nominated for the Academy’s best animated feature award.
This year the five nominees for the best animated feature Oscar also received Annie nominations, though eventual Oscar recipient Brave lost the top Annie prize to Wreck-It Ralph.
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