A new Pd(II) coordination compound, [Pd(L)(PPh3)2] (1) [H2L = benzil bis(pyridyl hydrazone] has been synthesized and characterized by using spectroscopic (FT-IR, electronic, and NMR) and single crystal X-ray diffraction confirming that Pd(II) coordination compound (1) preferred a distorted square planar geometry. In the crystal structure of 1, supramolecular networks have been developed by involving the association of C–H⋅⋅⋅π, intermolecular C–H⋅⋅⋅N interactions, C–O⋅⋅⋅H, and π⋅⋅⋅π interactions. Theoretical investigations have been carried out to understand the interactions within 1. Molecular docking study confirms strong hydrophilic interactions of 1 with the polar moiety of the amino acids in 1. The antitumor activities of Pd(II) complex (1) and the ligand were studied in vitro and in vivo using Dalton’s lymphoma malignant cancer model. Pd(II) complex (1) induced concentration-dependent cytotoxicity and apoptotic cell death leading to a decrease in cell viability, body weight, and tumor volume in mice. Mice treated with 1 showed an increase in life span with a mean survival period of 25 days. Furthermore, an in silico molecular interaction study supports the wet lab results.