Ginkgolide B (GB) and Puerarin (Pue) are active pharmaceutical ingredients for the treatment of Parkinson’s disease (PD); however, both are poorly water-soluble, which limits their bioavailability. The present study used the niosome vesicle encapsulation technique to prepare a novel GB composite drug. The conditions for GB–Pue niosomal complex preparation were as follows: a hydration temperature of 60°C, a hydrophilic–lipophilic balance of 10.5, a drug–carrier mass ratio of 8:100, and a surfactant–cholesterol mass ratio of 1.5:1. The niosomal complex suspension was uniformly distributed and milky white in color, with no stratification over a duration of 1 month. It had an average particle size of 187.3 nm, a particle-size distribution of 0.237, a GB encapsulation efficiency (EE) of 68.2%, a GB drug-loading rate of 90.1%, a Pue EE of 40.5%, and a Pue drug-loading rate of 83.3%. The optimal storage temperature for the niosomal complex suspension was 4°C. Following an intravenous injection of the niosomal complex suspension into the rat tail, the area under the curve (AUC) from 0 to 4 h was 54.1 h µg mL−1, with a mean residence time (MRT) of 0.96 h, a distribution half-life (T1/2α) of 0.195 h, and a total clearance of 0.003 L h−1 kg−1. The AUC and MRT of the composite prescription were 1.1- and 1.4-times those of the commercial injection, respectively, showing significantly increased sustained release and bioavailability. Moreover, the distribution of GB in the brain tissue was 1.8-times that of the commercial injection. In conclusion, the novel GB niosomal composite drug, with excellent stability, improved pharmacokinetics, and brain tissue distribution, demonstrates great potential for the delivery of GB and Pue for PD therapeutics.