The aim of this research is to examine the potential anticancer properties of thymoquinone (TQ)-encapsulated selenium nanoparticles (TQ-SeNPs) in HEC1B endometrial carcinoma cells. TQ-SeNPs were synthesized, and their size, morphology, and elemental analysis were characterized. Morphological changes were examined by using scanning electron microscopy (SEM). The cytotoxicity and viability of nanothymoquinone were assessed by the XTT (2,3-bis (2-methoxy-4-nitro-5sulfophenyl)-2H-tetrazolium-5 carboxanilide) assay. Gene expressions and protein levels of the mitogen-activated protein kinase (MAPK) signaling pathway were analyzed by real-time PCR and enzyme-linked immunosorbent assay (ELISA), respectively. The decrease in the viability of HEC1B endometrial carcinoma cells was observed in a time-and dose-dependent manner. HEC-1B cells were treated with TQ-SeNP at 40−640 μg/mL concentrations and time intervals, and their viability was assessed by XTT assay. IC 50 doses of TQ-SeNP in HEC1B cells were detected as 526.45 μg/mL at 48th hour. ELISA indicated that TQ-SeNP treatment reduced the level of p38 MAPK. ERK2, MEK2, and NFKB (p65) mRNA expressions were decreased in the dose group administered TQ-SeNP at the 48th hour compared to that in the control group. However, it was not significant. The novel nanoparticle showed an antiproliferative effect in endometrial cancer cells. However, further studies are needed to increase the anticancer activity of the cell in the TQ-SeNP interaction.