Aim: To evaluate the retention rate of self-adhering flowable composite as fissure sealant in comparison with the unfilled resin sealant on first permanent molars of 6–9-year-old children. Materials and methods: A 2-arm, split-mouth randomized controlled trial included 100 children of age 6–9 years with completely erupted mandibular first permanent molars. A total of 200 teeth were randomly divided into two groups, group I: self-adhering flowable composite; group II: unfilled resin sealant. Sealants were placed on the mandibular first permanent molars and the children were recalled at 6, 12, and 18 months intervals to evaluate the retention rate. Chi-square test was used to analyze the data. Results: Self-adhering flowable composite has shown a complete retention rate of 67%, 47%, and 46% at 6, 12, and 18-month intervals, respectively, whereas unfilled resin sealant has shown 41%, 8%, and 5% retention rate at 6, 12, and 18-month intervals, respectively. The difference in the complete sealant retention rates between the groups is found to be statistically highly significant at all the follow-up intervals (p = 0.0004, 0.0001, and 0.0001 at 6, 12, and 18-month intervals, respectively). In both groups, maximum sealant loss occurred between 6 and 12-month intervals. Retention rates were higher at 6 months intervals which were significantly reduced over 18 months intervals. Conclusion: Self-adhering flowable composite has shown a higher retention rate compared to unfilled resin sealant at all the time intervals. The retention rate of both materials decreased with time. However, the loss of sealant was more with unfilled resin sealant. Clinical significance: In pediatric dental practice, the elimination of a step in restorative dentistry protocol makes a big difference as time is a critical factor in obtaining children's cooperation. The use of self-adhering materials eliminates the step of bonding agent application, which simplifies the restorative protocol and makes the clinical practice effective. Therefore, these self-adhering flowable composite resin materials can be considered fissure sealants in routine clinical practice.