Non-obstructive azoospermia (NOA) is often associated with genetic variants. Whole-exome sequencing (WES) has emerged as a powerful tool in studying the genetic diagnosis of NOA and to help identify novel causal gene variants. Minichromosome maintenance domain-containing 2 (MCMDC2), an atypical yet conserved MCM protein, plays a key role in meiotic recombination and the maintenance of fertility. To date, only a limited number of MCMDC2 variants have been reported. The current study identified a novel deleterious variant (c.G226T/p.Val76Phe) of MCMDC2 by WES in a patient with NOA from a consanguineous Chinese family. Bioinformatics analysis indicated that the altered amino acid is highly conserved, and the c.G226T/p.Val76Phe variant may affect the structure and function of the MCMDC2 protein. Our results provide new insights into the underlying etiology of NOA in humans, further expanding the mutant spectrum of MCMDC2.