This study evaluated the impact of photobiomodulation (PBM) combined with glass ionomer sealant on hypersensitivity, oral hygiene, and sealant retention in molars affected by molar incisor hypomineralization (MIH). Forty-nine children (6-12 years) with MIH (Grade 3, 4a, or 4b) per MIH-TNI criteria were randomly assigned to two groups: control (n = 25, fluoride toothpaste, sealant with self-curing glass ionomer cement, simulated PBM) and treatment (n = 24, fluoride toothpaste, sealant with self-curing glass ionomer cement, active PBM). Hypersensitivity (SCASS, VAS), oral hygiene (OHI-S), and sealant retention (CCC system) were assessed. Forty-six children completed the study and were evaluated. At all post-baseline time points, the treatment group showed significantly lower VAS and SCASS scores (p < 0.05). OHI-S improved in both groups, with a positive correlation between reduced hypersensitivity and better oral hygiene. Sealant retention was higher in the treatment group after 30 days, with 56.5% of teeth showing complete retention versus 17.4% in the control group (p = 0.002). In the control group, greater hypersensitivity correlated with worse retention. PBM combined with glass ionomer cement reduces hypersensitivity, improves oral hygiene, and enhances sealant retention in MIH-affected molars. The combined treatment provides superior results in hypersensitivity reduction and sealant retention compared to sealant alone, offering a more effective approach for managing MIH.Trial registration: NCT05370417 in ClinicalTrials.gov.