5-(Tert-butyl)-N-(2,4-dichlorophenyl)-1H-1,2,4-triazol-3-amine was synthesized in four steps starting from pivalic acid via thiourea formation followed by heterocyclization with hydrazine hydrate. The structure was established by spectroscopic data, elemental analysis, and substantiated by single-crystal X-ray crystallography. It crystallizes in orthorhombic crystal system with Pbca as space group. In crystal structure, the intermolecular N–H···N hydrogen bonds link the molecules which stabilize the structure. Density functional theory (DFT) calculations have been performed to gain insights into the electronic structure of the compound. The inhibitory activity of the compound against the Jack bean urease revealed significant inhibition IC50 value 0.21 ± 0.2 μM (~ 100-folds higher than standard). The Hirshfeld surface is an external 3D curve of electrostatic potential in space over a particular molecule in crystalline state. Hirshfeld surface analysis and 2D fingerprint plots were performed. The evaluation of the electrostatic, dispersion, and total energy frameworks indicates that the stabilization is dominated via the electrostatic energy contribution. The molecular docking of compound exhibited hydrogen bonding and C-H-π interaction with docking energy score of − 6.68 and − 6.46 kcal/mol respectively. The compound was also evaluated for antioxidant scavenging activities against DPPH and showed promising antioxidant property with an IC50 value of 0.45 μg/mL. In addition, the compound was also tested for cytotoxicity using brine shrimp lethality bioassay and LD50 was found to be 0.5 μg/mL. DNA protection assay was performed with human blood DNA and DNA cleavage was protected by compound at or above 6 μM concentration. Furthermore, DNA titration by UV-visible spectroscopy for compound’s interaction with DNA revealed substantial (Kb; 1.605 × 103 M−1) and spontaneous (ΔG; − 19.023 kJmol−1) interaction via intercalation and the linear rise in DNA viscosity in the presence of compound’s concentrations further verified the intercalation binding mode.