This study presents a nanoscale encapsulation approach using a hybrid system of cetyltrimethylammonium bromide (CTAB) and sodium carboxymethyl cellulose (NaCMC) to improve the solubility, stability, and antifungal activity of Reetha (Sapindus mukorossi) seed extract (RE). UV–Vis spectroscopy confirmed effective solubilization of saponins and phenolics by CTAB, while NaCMC provided additional stability through electrostatic and steric interactions. Binding studies showed strong interactions in both CTAB (Kb = 2.790) and CTAB-NaCMC (Kb = 3.079) systems. The CTAB-NaCMC system achieved higher encapsulation efficiency (EE% = 7.243 mg). Dynamic light scattering (DLS) analysis indicated a particle size of 255.9 d.nm. Transmission electron microscopy (TEM) further revealed uniform, well-dispersed nanostructures. Antifungal assays against Rhizoctonia solani showed up to 66.7% growth inhibition, due to the combined effects of CTAB and NaCMC. Overall, the CTAB-NaCMC hybrid system offers a promising, eco-friendly platform for enhancing the delivery and efficacy of plant-based bioactives.