A new series of 4-benzyl-6,7,8,9-tetrahydro[1]benzothieno [3,2-e] [1,2,4]triazolo [4,3-a]pyrimidines was synthesized motivated by the widely reported anticancer activity of thieno [2,3-d]pyrimidines and triazolothienopyrimidines. The in vitro cytotoxic activity of some selected compounds was evaluated against two human cell lines: prostate cancer (PC-3) and colon cancer (HCT-116). A preliminary study of the structure-activity relationship of the target compounds was discussed. Most of the synthesized compounds showed remarkable activity on the tested cell lines, while compound 16c had the highest potency against the PC-3 cell line with an IC 50 of 5.48 μM compared to Doxorubicin (IC 50 = 7.7 μM), the reference standard used in this study. On the other hand, 6c and 18c were the most active against HCT-116 (IC 50 = 6.12 and 6.56 μM, respectively) relative to IC 50 = 15.82 μM of the standard. Thus, some of the synthesized thienopyrimidine derivatives, specially 6c, 16c and 18c, have the potential to be developed into potent anticancer agents.