: Root-end filling materials are typically used following endodontic surgeries, and due to their different chemical compositions, they have varying effects on the survival and differentiation of tissues around the root apex. The purpose of this in vitro study was to evaluate the effects of three retrograde filling materials—ProRoot MTA, Super ethoxy benzoic acid (EBA), and Geristore—on the production of pro-inflammatory and resorptive cytokines (RANK, RANK-L, OPG, IL-1β, and TNF-α). After mixing and setting, the experimental materials were exposed to UV rays and then applied to the prepared cells. This study used osteoblast (MG-63) and THP-1 monocyte cell lines, as well as peripheral blood monocytes (PBM). The evaluation times for RANK-L and OPG were 24 and 48 hours, while IL-1β and tumor necrosis factor (TNF-α) were evaluated at 24 hours. The RANK levels were measured using flow cytometry, and monocyte survival was assessed at different times using the MTT assay. The results were analyzed using Minitab statistical software, which indicated that the type of material significantly affected cytokine production. Exposure of monocytes to EBA resulted in a decrease in TNF-α and IL-1β secretion compared to the other groups. However, in the THP-1 cell line, there was no significant difference in the release of pro-inflammatory cytokines between the groups. Conversely, Geristore induced the highest level of RANK-L and the lowest level of OPG in cultures with the MG-63 cell line. According to the MTT assay, the viability order of the materials from early to late was Geristore < EBA < MTA.