Statement of the Problem: There are some concerns regarding the effect of chlorhexidine (CHX) applied for cavity disinfection on the bond strength of adhesive restorations to dentin.Purpose: This study sought to assess the effect of CHX on the shear bond strength (SBS) of Equia resin-modified glass ionomer cement (RMGIC) to dentin in permanent teeth.Materials and Method: In this experimental study, the buccal surface of 84 freshly extracted human premolars was ground to expose the flat dentin. The samples were randomly assigned to four groups (n=21). The steps were as following in the group Ia: conditioning, Equia RMGIC, 500 thermal cycles; group Ib: conditioning, Equia RMGIC, 6000 thermal cycles; group IIa: conditioning, CHX, Equia RMGIC, 500 thermal cycles, and group IIb: conditioning, CHX, Equia RMGIC, and 6000 thermal cycles. Twenty samples from each group were subjected to SBS test and one sample was inspected under a scanning electron microscope. Data were analyzed using two-way ANOVA and t-test.Results: The SBS was significantly different among the groups (p= 0.007). The groups subjected to 500 thermal cycles showed significantly higher SBS to dentin when they were treated with CHX (p= 0.000). There was no significant difference between samples thermocycled for 6000 cycles with and without application of CHX (p= 0.269). The SBS in the groups that were thermocycled for 6000 cycles (Ib and IIb) was lower than those thermocycled for 500 cycles (Ia and IIa). This difference between IIa and IIb was statistically significant (p= 0.007).Conclusion: Chlorhexidine can positively affect the short term SBS of Equia RMGIC to dentin.