What attracted Jim Carrey to this role more than anything else was the chance to dance with penguins like his hero Dick Van Dyke did in Mary Poppins (1964).
Real penguins were used for certain shots and most of the scenes took place in a refrigerated set.
In the source novel, Mr. Popper forms a vaudeville act called "Popper's Performing Penguins". This story element was considered as a movie plot, but ultimately not used.
Ben Stiller was originally cast as Mr. Popper. Reportedly, Stiller withdrew from this movie after original director Noah Baumbach left. Jack Black and Owen Wilson were considered to replace him.
There are six main penguins who feature in this movie, but in the source novel, there were twelve. Most were named after historical Navy Captains: Cook, Nelson, Columbus, et cetera.