The intermolecular interaction between 2-(N-phenyl-N-methyl)aminonaphtho-1,4-quinone (1) and 2-(4-N-methylaminophenyl)naphtho-1,4-quinone (2) and human serum albumin (HSA) was investigated using spectroscopic techniques combined with in silico calculations via molecular docking. Steady-state titration of HSA fluorescence by 1 and 2 (λexc 295 nm) in PBS at 305, 310, and 315 K, as well as studies employing time-resolved fluorescence emission, demonstrated that the HSA:1 and HSA:2 interaction occurs through a static quenching mechanism. The Stern-Volmer constant (Ksv) values, (1.56 ± 0.08) and (3.05 ± 0.10) × 104 L/mol at 310 K for HSA:1 and HSA:2, respectively, indicate a moderate binding affinity. Van't Hoff plots showed that HSA:1 and HSA:2 interactions are spontaneous (negative ΔGo) with a hydrophobic character (ΔSo value of 0.00707 ± 0.00106 and 0.0392 ± 0.0062 kJ/mol K for HSA:1 and HSA:2, respectively) and specific electrostatic interactions (ΔHo value of –22.7 ± 3.3 and −14.4 ± 1.9 kJ/mol for HSA:1 and HSA:2, respectively). Synchronous fluorescence results showed significant perturbation in the microenvironment of the tryptophan residue (Trp-214). Circular dichroism indicated that after interaction with naphthoquinones 1 and 2, the HSA structure remains predominantly in the α-helix form. Finally, molecular docking revealed the formation of hydrophobic, electrostatic, and hydrogen bond interactions with the surrounding amino acid residues in subdomain IIA of HSA, which contains the Trp-214 residue, validated with the experimental drug-displacement assays. Overall, spectroscopic and in silico characterization of HSA:1 and HSA:2 might reflect in a low half-life in the human bloodstream, indicating the necessity of methods to improve the bioavailability, e.g., studies on the type of administration (oral versus intravenous).