Background: Sprint interval training (SIT) performed on a cycle ergometer is a common mode of training and has become increasingly studied as an exercise intervention to improve a range of physical performance outcomes. Objectives: The primary objective was to synthesise findings from published research and through meta-analysis quantify the effect of SIT and potential moderators on physical performance outcomes with healthy adults. The secondary objective was to assess the methodological quality of included studies and the existence of small study effects. Methods: The review included studies from 2000 to 2020 based on the following criteria: 1) healthy participants 18 to 45 years; 2) minimum 2-week SIT intervention comprising “all out” sprints up to a maximum of 30 seconds on a cycle ergometer; 3) cohort or control group design; 4) pre-post intervention outcomes that could be categorised as aerobic (e.g. VO2max, incremental time); anaerobic (e.g. peak power, fatigue index); mixed aerobic/anaerobic (e.g. critical power test, peak power across repeated tests); or muscular force (e.g. maximal voluntary contraction, peak force). Methodological quality was assessed using a modified Downs and Black Checklist and a strategy based on the recommendations of the Grading of Recommendations Assessment Development and Evaluation working group. All meta-analyses were conducted within a Bayesian framework to facilitate probabilistic interpretations of mean standardised effect sizes obtained from both non-controlled and non-exercise-controlled data. Results: Fifty-five studies met the inclusion criteria, with 50% graded as moderate methodological quality and 42% graded as low methodological quality. Most studies (58%) comprised an intervention of 4 weeks or less, with the collective research featuring a wide range of training protocols. The primary meta-analysis was conducted on non-controlled effect sizes from 403 outcomes. The analysis identified a small to medium effect of improved physical performance with SIT (ES0.5 = 0.43 [95%CrI: 0.35 to 0.52]). Moderator analyses identified large differences among outcome types, with no evidence of an effect for muscular force outcomes (ES0.5 = 0.05 [95%CrI: -0.25 to 0.35]) and the largest effect estimated for anaerobic outcomes (ES0.5 = 0.57 [95%CrI: 0.33 to 0.86]). Additionally, moderation effects were identified for intervention duration, sprint length, and the number sprints performed per session, with larger effects obtained for greater values of each moderator. Many positive outliers were identified with additional evidence of extensive small study effects. Conclusion: This meta-analysis demonstrates that short-term SIT interventions are effective for developing small to moderate improvements in a range of physical performance outcomes across the aerobic to anaerobic spectrum. However, extensive small study effects, likely influenced by researchers analysing many outcomes, suggests potential overestimation of reported effects. It is recommended that future research analyse a smaller number of a priori selected outcomes and investigate models to progress SIT interventions for longer-term performance improvements.