Northern Territory Police are hunting for a crocodile napper, after a pet freshwater croc was stolen was stolen from a Darwin daycare centre.

Courtney Ramage, one of the workers at Kids Force Child Care Centre in Eaton, said she noticed Barney wasn't in his tank this morning.

"Had a look in the yard, he wasn't out in the yard," she said.

"Kids went for a bit of a treasure hunt to see if we could find him and still no Barney.

"We pulled everything out of the tank and we're searching around and then we came down and the art shed door was open and we're like 'what's going on here'?

"We've noticed that the box is gone and nothing else has been touched, so (they've) obviously put the croc in the box and taken off."

Police believe the baby freshwater croc was taken from the centre overnight.

The crocodile has lived at the childcare centre for less than year.

Centre director Belinda Murray said the croc had been bought to distract children who were frightened about leaving their parents for the first time.

"It was just something different that's why we got him instead of having the usual chickens or what not we just decided that we'd get a crocodile," Ms Murray said.