Background: Colorectal cancer (CRC) is the third most common cancer worldwide. Recently, mesenchymal stem cells (MSCs) have been considered a suitable cell therapy option for cancer due to their high migration rate to the tumor site. Objectives: The study aimed to compare the effects of human umbilical cord blood derived-MSC (UCMSC) and human Wharton’s Jelly derived-MSC (WJ-MSC) on the HT-29 cell line. Methods: UC-MSC was obtained by Ficoll-Paque density gradient and WJ-MSC by explant method. The characterizations of MSCs and apoptosis assays were performed by flow cytometry, and caspase-3 protein levels were measured by ELISA. Results: After 72 hours of HT-29 cancer cells incubation, it was indicated that WJ-MSC was more effective at 1:5 and 1:10 ratios. Similar results were found for caspase-3 by ELISA. Moreover, WJ-MSC (1:5, p < 0.006; 1:10, p < 0.007) was found to be more effective at both doses compared to UC-MSC. Conclusion: In this study, we used two different MSC sources at two different ratios to evaluate the apoptotic effect of MSC in vitro on HT-29 CRC cells. As a result, WJ-MSC indicated a more apoptotic effect on HT-29 cells compared to CB-MSC. We anticipated that this preliminary in vitro study would be extended in future in vitro/in vivo studies. Moreover, investigating the behavior of MSC in colorectal tumor microenvironment will be beneficial for the stem cell therapy approach.