The addition of chlorhexidine (CHX) to a resinous experimental Mineral Trioxide Aggregate (E-MTA) based root-end filling material is an alternative to boost its antimicrobial activity. However, the influence of chlorhexidine on the properties of this material is unclear. The aim of this study was to evaluate the influence of 2% chlorhexidine on the pH, calcium ion release and setting time of a Bisphenol A Ethoxylate Dimethacrylate/Mineral Trioxide Aggregate (Bis-EMA/MTA) based dual-cure experimental root-end filling material (E-MTA), in comparison with E-MTA without the addition of CHX and with conventional white MTA (W-MTA). The materials were placed in polyethylene tubes, and immersed in deionized water to determine pH (digital pH meter) and calcium ion release (atomic absorption spectrometry technique). The setting time of each material was analyzed using Gilmore needles. The data were statistically analyzed at a significance level of 5%. E-MTA + CHX showed an alkaline pH in the 3 h period of evaluation, the alkalinity of which decreased but remained as such for 15 days. The pH of E-MTA + CHX was higher than the other two materials after 7 days, and lower after 30 days (p < 0.05). All of the materials were found to release calcium ions throughout the 30 days of the study. The addition of CHX increased the calcium ion release of E-MTA to levels statistically similar to W-MTA. E-MTA showed shorter initial and final setting time, compared with W-MTA (p < 0.05). The addition of 2% CHX to MTA prevented setting of the material. The addition of CHX to E-MTA increased its pH and calcium ion release. However, it also prevented setting of the material.