Over the past years, the assessment of myco-fabricated selenium nanoparticles (SeNPs) properties, is still in its infancy. Herein, we have highly stable myco-synthesized SeNPs using molecularly identified soil-isolated fungus; Penicillium tardochrysogenum OR059437; (PeSeNPs) were clarified via TEM, EDX, UV–Vis spectrophotometer, FTIR and zeta potential. The therapeutic efficacy profile will be determined, these crystalline PeSeNPs were examined for antioxidant, antimicrobial, MIC, and anticancer potentials, indicating that, PeSeNPs have antioxidant activity of (IC50, 109.11 μg/mL) using DPPH free radical scavenging assay. Also, PeSeNPs possess antimicrobial potential against Penicillium italicum RCMB 001,018 (1) IMI 193,019, Methicillin-Resistant Staphylococcus aureus (MRSA) ATCC 4330 and Porphyromonas gingivalis RCMB 022,001 (1) EMCC 1699; with I.Z. diameters and MIC; 16 ± 0.5 mm and MIC 500 µg/ml, 11.9 ± 0.6 mm, 500 µg/ml and 15.9±0.6 mm, 1000 µg/ml, respectively. Additionally, TEM micrographs were taken for P. italicum treated with PeSeNPs, demonstrating the destruction of hyphal membrane and internal organelles integrity, pores formation, and cell death. PeSeNP alone in vivo and combined with a near-infrared physiotherapy lamp with an energy intensity of 140 mW/cm2 showed a strong therapeutic effect against cancer cells. Thus, PeSeNPs represent anticancer agents and a suitable photothermal option for treating different kinds of cancer cells with lower toxicity and higher efficiency than normal cells. The combination therapy showed a very large and significant reduction in tumor volume, the tumor cells showed large necrosis, shrank, and disappeared. There was also improvement in liver ultrastructure, liver enzymes, and histology, as well as renal function, urea, and creatinine.