Reactions between sodium tetrachloropalladate and 2‐ (or 4‐) substituted 4‐phenyl‐3‐thiosemicarbazone ligands (HLR), with various electron‐donating and electron‐withdrawing substituents (R = OCH3, NO2, and Cl), afford square‐planar complexes of the general formula [Pd(LR)2]. Ground‐state geometry optimization and the vibrational analysis of cis‐ and trans‐isomers of the complexes were carried out to get an insight into the stereochemistry of the complexes. Natural bond orbital analysis was used to analyze how the nature of the substituent affects the natural charge of the metal center, the type of hybridization, and the strength of the M−N and M−S bonds. Using spectrophotometry, the stability of the complexes, and their DNA binding abilities were assessed. The Pd(II) complexes showed moderate cytotoxicity against HepG‐2 and Caco‐2 cell lines, two of the assessed malignant cell lines, resulting in all known cell death types, including early apoptotic bodies and late apoptotic vacuoles as well as evident necrotic bodies.