Baicalein (BCL) has poor oral bioavailability owing to low solubility and extensive metabolism. This study developed a honey-based BCL-loaded nanoemulsion (HB-BCL-NE; 10% w/w honey) and compared it with a honey-free nanoemulsion (HF-BCL-NE) and BCL suspension (BCL-Susp). Physicochemical properties, in vitro release, and four-week refrigerated stability were assessed. After oral dosing in rats (30 mg/kg), free and total BCL were quantified by validated LC–MS/MS; plasma pharmacokinetics were evaluated over 24 h (n = 5), and tissue concentrations at 4 h (n = 3). HB-BCL-NE showed smaller droplets (66.7 ± 0.30 vs 74.2 ± 1.02 nm), a more negative zeta potential (−34.3 ± 0.72 vs −30.03 ± 0.15 mV), and higher encapsulation efficiency (69.91 ± 0.90% vs 67.51 ± 0.41%) than HF-BCL-NE. After four weeks, its droplet size remained lower (73.3 ± 1.47 vs 90.2 ± 1.45 nm). HB-BCL-NE showed higher BCL release than HF-BCL-NE at later time points at pH 6.8, whereas no difference at pH 1.2. Its free-BCL AUC_inf was 2.4- and 5.8-fold higher than HF-BCL-NE and BCL-Susp, respectively; total-BCL AUC_inf was 2.0- and 5.7-fold higher. It also yielded the highest mean tissue concentrations. Honey therefore improved nanoemulsion stability and systemic and tissue exposure, supporting its use as a natural functional excipient for oral delivery.