Although many studies in recent years have examined the use of gamification as a motivational strategy in education, evidence regarding its effects on intrinsic motivation is inconsistent. To make the case for or against the adoption of gamification in education, this study examines its effects on students' intrinsic motivation and the underlying motivational factors: perceived competence, autonomy, and relatedness. In this review, we analyzed the results of studies comparing gamified learning with non-gamified learning published between 2011 and 2022. The results of our meta-analysis of 35 independent interventions (involving 2500 participants) indicated an overall significant but small effect size favoring gamified learning over learning without gamification (Hedges' g = 0.257, 95% CI [0.043, 0.471], p = 0.019) with no evidence of publication bias. Gamification also exerted a positive and significant effect on the students' perceptions of autonomy (Hedges' g = 0.638, 95% CI [0.139, 1.136], p = 0.012) and relatedness (Hedges' g = 1.776, 95% CI [0.737, 2.814], p = 0.001), but minimal impact on competence (Hedges' g = 0.277, 95% CI [0.001, 0.553], p = 0.049). To further investigate the possible reasons for the small impact on intrinsic motivation, a systematic review of 31 studies was conducted. The findings revealed two major challenges encountered in the adoption of gamification to increase students' intrinsic motivation: students' lack of perceived competence and lack of perceived autonomy in gamified classes.