Emerging evidence shows an association between protein intake during infancy and later obesity risk, and that association may differ by protein sources. This systematic review summarized and evaluated prospective cohort studies assessing the long-term association of total protein intake and protein sources during infancy (from birth to 2 y) with subsequent obesity outcomes in childhood or adolescence. Literature searches were conducted in Embase, Medline, Scopus, and Web of Science. Sixteen studies that reported associations between total protein intake and/or protein intake from different sources from birth to 2 y and ≥1 obesity outcomes in childhood or adolescence from 9 cohorts were identified. Most studies (11/16) were rated as high quality. The most frequently reported association was total protein intake and BMI (up to 10 y) with 6 out of 7 cohorts showing significant positive associations. Similar associations were found for animal protein, but not for plant protein. Limited studies examined the association between protein intake (both total and sources) and body composition (body fat, fat mass, and fat-free mass) and revealed inconsistent findings. Overall, higher intakes of total and animal protein during infancy were associated with higher BMI in childhood and adolescence. Future studies investigating the contribution of protein sources in long-term obesity development are needed. This review was registered at PROSPERO as CRD42020166540.