In this study various of thieno[3,2‐d]pyrimidine derivatives have been synthesized by treating different secondary amines through aromatic nucleophilic substitution reaction (SNAr) followed by Suzuki reaction with aryl and heteroaryl boronic acids. A bis‐Suzuki coupling was also performed to generate bis‐aryl thienopyrimidine derivatives. The synthesized compounds were screened for the hydrolytic activity of h‐NTPdase1, h‐NTPdase2, h‐NTPdase3, and h‐NTPdase8. The compound N‐benzyl‐N‐methyl‐7‐phenylthieno[3,2‐d]pyrimidin‐4‐amine 3 j selectively inhibits the activity of h‐NTPdase1 with IC50 value of 0.62±0.02 μM whereas, the compound 4 d was the most potent inhibitor of h‐NTPdase2 with sub‐micromolar IC50 value of 0.33±0.09 μM. Similarly, compounds 4 c and 3 b were found to be selective inhibitors for isozymes h‐NTPdase3 (IC50=0.13±0.06 μM) and h‐NTPdase8 (IC50=0.32±0.10 μM), respectively. The molecular docking study of the compounds with the highest potency and selectivity revealed the interactions with the important amino acid residues.