Background: Propolis is a natural resinous substance collected by honeybees, chiefly from buds and the leaves, branches, and bark of trees. Its role as a wound-healing gel has been studied, but the use of a propolis hydrogel in the treatment of dentinal hypersensitivity has not been evaluated. Dentin hypersensitivity (DH) is commonly treated via iontophoresis using fluoridated desensitizers. The aim of the present study was to compare and evaluate the effects of a 10% propolis hydrogel, 2% sodium fluoride (NaF), and 1.23% acidulated phosphate fluoride (APF) when used in conjunction with iontophoresis for the treatment of cervical dentin hypersensitivity (DH). Methods: Systemically healthy patients complaining of DH were selected for this single-centre, parallel, double-blind randomized clinical trial. Three substances were selected as desensitizers for study in the present trial: a 10% propolis hydrogel, 2% sodium fluoride, and 1.23% acidulated phosphate fluoride, all in conjunction with iontophoresis. Any decrease in DH following the application of specific stimuli was assessed at baseline, before and after application, on the 14th day following use, and on the 28th day following the intervention. Results: Intra-group comparisons show diminished values of DH at maximum post-op follow-up intervals which were significantly trimmed down from the baseline (p< 0.05). The 2% NaF demonstrated a significant reduction in DH over 1.23% APF and the 10% propolis hydrogel (p< 0.05). However, there was no statistically significant difference in the mean difference between the APF and propolis hydrogel groups assessed via tactile, cold, and air tests (p> 0.05). Conclusion: All three desensitizers have proved to be useful when used in conjugation with iontophoresis. Within the limitations of this study, a 10% propolis hydrogel can be used as a naturally occurring alternative to commercially available fluoridated desensitizers.