Restorative treatment for molars affected by molar incisor hypomineralization (MIH) presents a challenge due to the altered enamel structure. It is critical to understand the evidence base of the available restorative options, due to the high treatment burden for such teeth. This systematic review and meta-analysis aimed to evaluate and compare the success rates of glass ionomer cement (GIC) and composite resin restorations in hypomineralized first permanent molars and to further evaluate the restorations on the basis of modified United States Public Health Service (USPHS) criteria. This review was registered in International Prospective Register of Systematic Reviews (PROSPERO) database as CRD42024566898. Searches were conducted in PubMed, Google Scholar and Ebsco from January 2000 to May 2024. A total of 13 studies were included according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines in qualitative synthesis and meta-analysis. The over-all success rate was calculated for each study as the primary outcome. The success rates for different parameters of the modified USPHS criteria was calculated as secondary outcome. The Cochrane Collaboration's tool and risk of bias in non-randomized studies of intervention (ROBINS-I) tool were used to assess the risk of bias. The combined effect, heterogeneity and publication bias were analyzed using Stata 17.0 (StataCorp LLC, College Station, TX, USA). A p-value <0.05 was regarded as statistically significant. Composite resin restorations presented significantly superior results over GIC for overall success (p = 0.0004), marginal adaptation (p = 0.0124) and surface texture (p <0.0001). For the parameters such as retention (p = 0.06), secondary caries (p = 0.20), marginal discolouration (p = 0.3830) and colour match (p = 0.1440) composite resin performed better; however, the difference was statistically nonsignificant. Considering the constraints of this systematic review and meta-analysis, it can be recommended that composite resin restorations presented superior results over GIC for hypomineralized permanent first molars. Complete removal of the hypomineralized tissue is recommended.