Recent systematic reviews and meta-analyses conclude that similar social cognitive impairments are found in autism spectrum disorder (ASD) and schizophrenia spectrum disorder (SSD). While methodological issues have been mentioned as a limitation, no study has yet explored the magnitude of methodological heterogeneity across these studies and its potential impact for their conclusion. The purpose of this study was to systematically review studies comparing social cognitive impairments in ASD and SSD with a focus on methodology. Following the PRISMA guidelines, we searched all publications on PubMed, PsycINFO, and Embase. Of the 765 studies identified in our data base searches, 21 cross-sectional studies were included in the review. We found significant methodological heterogeneity across the studies. In the 21 studies, a total of 37 different measures of social cognition were used, 25 of which were only used in 1 study. Across studies, the same measure was often said to be assessing different constructs of social cognition – a confusion that seems to reflect the ambiguous definitions of what these measures test in the studies that introduced them. Moreover, inadequate differential diagnostic assessment of ASD samples was found in 81% of the studies, and sample characteristics were markedly varied. The ASD and SSD groups were also often unmatched in terms of medication usage and substance use disorder history. Future studies must address these methodological issues before a definite conclusion can be drawn about the potential similarity of social cognitive impairments in ASD and SSD.