Objectives The aim of this randomized clinical trial (RCT) was to explore the clinical survival of a new, Bis-GMA-free pit and fissure sealant (Helioseal F Plus) in comparison to an established control material (Helioseal F). Material and methods This in vivo study was designed as a prospective, 2-year, two-centre RCT with a split-mouth design. The initial study population consisted of 92 adolescents who were followed up 1 month (N = 89), 6 months (N = 88), 1 year (N = 85) and 2 years (N = 82) after sealant application. The attrition rate was 10.9% after 2 years. At each examination, the sealant retention and presence of caries were recorded. The statistical analysis included the calculation of Kaplan–Meier survival curves, log-rank tests and a Cox proportional hazard regression model. Results No adverse events during the application or any of the follow-up visits were documented. The proportion of completely intact sealants and those with minimal loss was almost identical in both groups at 85.9% (Helioseal F Plus) and 86.5% Helioseal F) after 2 years of observation. The regression analysis revealed operator dependency; no significant differences were found between the materials, the study centres, the chosen isolation technique and patient age or sex. Conclusion The newly developed sealant can be evaluated as at least equivalent in terms of survival and retention behaviour compared to the established control material. Clinical relevance The new sealant can be recommended for clinical use. With respect to the material properties (Bis-GMA-free, less light polymerisation time and better thixotropic behaviour), it offers additional advantages with clinical relevance.