This clinical trial aimed to evaluate and compare the retention and cariostatic effects of hydrophilic and hydrophobic resin-based sealants (RBSs) for sealing pits and fissures in the permanent molars of uncooperative children. A split-mouth and double-blind randomized clinical trial (RCT) was conducted among 6- to 9-year-old uncooperative children. One hundred and four sound mandibular and maxillary first permanent molars were randomly allocated to be sealed with group I (UltraSeal XT® hydro™) or group II (Helioseal-F) in 34 uncooperative children. Clinical evaluation was performed by two investigators using the Color, Coverage and Caries system to assess sealant retention and cariostatic effect at 3-, 6- and 12-month intervals. Data analysis was performed using Friedman's and Mann-Whitney U tests. The final analysis included 31 children with 49 pairs of teeth. No significant differences were observed between the retention and cariostatic effects of hydrophilic and hydrophobic RBSs at the 3-, 6- and 12-month intervals (p = 0.23, p = 0.638, and p = 0.706, respectively) (p = 0.175, p = 0.065, and p = 0.171, respectively). After 12 months of follow-up, the hydrophilic RBSs showed an outcome equivalent to that of conventional hydrophobic RBSs in terms of retention and cariostatic effects. Therefore, hydrophilic RBSs could be considered as the sealing material of choice when isolation is difficult, particularly in uncooperative children.