He has written highly cited papers on mechanism design,[3] combinatorial auctions,[4] the computational complexity of pseudorandom number generators,[5] and interactive proof systems,[6] among other topics.

Nisan won an ACM Distinguished Dissertation Award for his Ph.D. thesis, on pseudorandom number generators.

[8] In 2012 he won the Gödel Prize, shared with five other recipients, for his work with Amir Ronen in which he coined the phrase "algorithmic mechanism design" and presented many applications of this type of problem within computer science.

[9] He won the Knuth Prize in 2016 "for fundamental and lasting contributions to theoretical computer science in areas including communication complexity, pseudorandom number generators, interactive proofs, and algorithmic game theory".

[10] In 2018 he won the Rothschild Prize[11] and the EATCS Award for "his decisive influence on a range of areas in computational complexity theory and for algorithmic mechanism design, an elegant and rigorous computational theory that aptly informs economics".