Objectives: To evaluate the effectiveness of self-assembling peptide P11-4 (SAP P11-4) in remineralizing post-orthodontic non-cavitated enamel carious lesions (NcCLs), in comparison to fluoride varnish and no treatment approach. Materials and methods: Forty-five participants (18-30 years) were randomly assigned to three groups. Group 1 received SAP P11-4, group 2 received fluoride varnish, and group 3 received no treatment. Primary outcomes were assessed using QLF (ΔF, ΔQ and Area parameters) for fluorescence changes, with secondary outcomes including ICDAS scores and Nyvad criteria. Follow-ups were at 6 and 12 months. Results: There were significant increases in ΔF values in the SAP 11-4 group compared to fluoride varnish at both the 6th and 12th-month follow-ups (p<0.001). There was a significant reduction in lesion depth only within the fluoride varnish group at the 12th month (p=0.010). The lesion volume (ΔQ) showed a significant decrease in both the SAP P11-4 and control groups at the 12-month follow-up (p=0.028). A significant reduction in the lesion area was seen in the SAP P11-4 and control groups at 6 months, with no significant difference between these two groups at both the 6th and 12th-month follow-ups. The fluoride varnish group exhibited a significant reduction in lesion area at the 12th month (p=0.010). No significant differences in ICDAS scores were found between groups 1 and 2 at the 6th and 12th months. The Nyvad criteria analysis revealed more lesions transitioning from active to inactive status in the SAP P11-4 and fluoride varnish groups (24 lesions per group) compared to the control group (20 lesions) at the 6-month follow-up. Conclusions: SAP P11-4 demonstrated superior remineralizing effectiveness compared to fluoride varnish and no treatment approach in managing NcCLs, as measured with QLF technology. However, all remineralizing treatments had a similar visual effect in masking the non-cavitated lesions.