Ulva selenium nanoparticles (USeNPs) were synthesized and characterized, then examined for their wound healing capacity through in vitro assay showing promising healing (82.27%) with USeNPs concentration (500 µg/mL). We also determined the antifungal potential via agar well diffusion technique, minimum inhibitory concentration (MIC), which was evaluated by a micro-dilution assay.  The synergistic effect of the USeNPs individually or in combination with standard antifungal antibiotic (ketoconazole;100 μg/mL) was studied against Cryptococcus neoformans RCMB 0049001 and Candida lipolytica RCMB 005007(1). Geotrichum candidum RCMB 041001 was also checked by agar well diffusion assay, followed by transmission electron microscopy to assess different changes in the most sensitive fungal yeast cells. The results indicated that USeNPs have a promising antifungal effect against C. neoformans RCMB 0049001 and C. lipolytica RCMB 005007(1) by achieving remarkable inhibition zones. In comparison, no effect was detected on G. candidum RCMB 041001. The MIC was found to be 8.1 μg and 312.5 μg for C. neoformans RCMB 0049001 and C. lipolytica RCMB 005007(1), respectively. The biosynthetic USeNPs have a strong antifungal potential and can elevate and strengthen the action of ketoconazole antibiotic towards different fungal pathogens, and this was obvious in the synergetic experiment carried out in the present study based on combining ketoconazole;100 μg/mL with USeNPs, which resulted in a detached C. neoformas RCMB 0049001 cells with a severe dramatic change.