Background: Tuberculosis (TB) remains a leading cause of global mortality, with 1.25 million deaths reported in 2023. Extended treatment duration contributes to poor patient adherence and treatment failure. Innovative drug delivery platforms are needed to improve therapeutic outcomes. Objective: This study aimed to develop nanoemulsions co-encapsulating quercetin and rifampicin and evaluate their physicochemical properties and in vitro biological activity relevant to TB therapy. Methods: Nanoemulsions (NEs) were prepared via hot solvent diffusion and phase inversion temperature techniques. Physicochemical characterization, stability, anti-inflammatory effects in BEAS-2B cells, and antimycobacterial activity against Mycobacterium tuberculosis H37Rv and resistant strains were assessed in vitro. Results: The quercetin-rifampicin nanoemulsion (QUE-RIF-NE) showed an average size of 24 nm, zeta potential of −27 mV, and drug recovery rates of 77% (quercetin) and 75% (rifampicin). The formulation was stable and non-cytotoxic at 10⁻⁸ M, reducing IFN-γ production by half and reactive oxygen species production by almost 75% in BEAS-2B cells. It also exhibited antimycobacterial activity against both susceptible and resistant M. tuberculosis strains (MIC ≤ 0.015 µg/mL). Conclusions: QUE-RIF-NE exhibits promising physicochemical stability and dual anti-inflammatory and antimicrobial activity in vitro, demonstrating potential for optimized pulmonary or systemic TB therapy that integrates both anti-inflammatory and antimicrobial effects.