Systematic reviews of single-case experimental research (SCER) in special education often use the What Works Clearinghouse (WWC) Standards to assess the methodological rigor of studies within a given literature base. While significant changes were made between the two most recent versions of the WWC standards, no research to date has evaluated the extent to which these standards would result in different evaluation outcomes. To examine potential differences, we applied version 4.1 and 5.0 of the standards to a sample database of SCER addressing the challenging behavior of students with autism in general education settings. Systematic search, screening, and review procedures resulted in a total of 20 articles included for this review. Findings indicated a 27% change in overall ratings across the studies, with version 5.0 leading to lower ratings than version 4.1, due to factors such as a lack of assessment of procedural fidelity, therapeutic baseline trends, and insufficient data points in the first baseline phase. We discuss implications for research based on our findings and recommend future directions for SCER in the field of special education.