This study presents a novel approach to manage vaginal infections due to Candidiasis, utilizing a novel silver secnidazole nano‐hybrid emulsion (Ag‐Secn‐NHE)‐based probiotics and free Ag‐Secn‐NHE. Ag‐Secn‐NHE was prepared by simple homogenization‒ultrasonication technique and validated by using a ultraviolet‒visible scan, dynamic light scattering, transmission electron microscopy (TEM), Fourier‐transform infrared spectroscopy, and zeta potential. Saccharomyces cerevisiae (RCMB 002Y001) is the most effective probiotic‐producing organism that demonstrates significant effects when combined with Ag‐Secn‐NHE. Ag‐Secn‐NHE‐based probiotics showed significant antifungal effect compared to free Ag‐Secn‐NHE, silver nitrate, silver nanoparticles, secnidazole, secnidazole nanoemulsion, and commercial vaginal wash against multidrug‐resistant vaginal pathogens. The highest inhibitory effect was achieved with Ag‐Secn‐NHE‐based probiotic against Candida auris, Candida albicans, and Cryptococcus neoformans with minimal inhibitory concentration (MIC) 0.625 ± 0.002, 0.00625:1.25 ± 0.012 and 0.00625:1.25 ± 0.032 mg/mL, respectively, in comparison with Ag‐Secn‐NHE that show MIC at 0.00625:1.25 ± 0.612, 0.0125:2.5 ± 0.812, and 0.0125:2.5 ± 0.112 mg/mL (Ag:Secn). Ag‐Secn‐NHE‐based‐ probiotic show minimum fungicidal concentration (MFC) at range from 2.5 to 20 mg/mL, wherever free Ag‐Secn‐NHE show MFC range from 5 to >20 mg/mL. Additionally, Ag‐Secn‐NHE‐based probiotics have 75% inhibition of biofilm formation against C. auris and 60% inhibition of biofilm formation against both Cryptococcus neoformans and C. albicans in comparison with free Ag‐Secn‐NHE. Time‐kill curves showed that the antifungal effect of Ag‐Secn‐NHE‐based probiotics was fungistatic at 2MIC value after 4 h and after 16 h for Ag‐Secn‐NHE. TEM photographs showed that C. auris cells treated with Ag‐Secn‐NHE‐based probiotic formula revealed severe deformations and distored ultrastructural changes. furthermore, results indicated that the Gamma radiation up to 15 kGy increases production of Ag‐Secn‐NHE in comparison with non‐irradiated one.