Natural products are promising drug candidates with various pharmacological effects. However, they can be difficult to use due to poor bioavailability or low stability. In this experiment, while developing topical formulations containing 0.1% Agrimonia pilosa extract, a simple and rapid method of analyzing flavonoid glucuronides, which are representative ingredients, was developed and validated, and the physicochemical properties and stability of flavonoid glucuronides were observed. As a result, an optimized cream formulation was developed. The oil phase comprised tween 60, liquid paraffin, propylene glycol, cetanol, stearyl alcohol, span 60, benzyl alcohol, and A. pilosa extracts, and the water phase comprised water and citric acid hydrate. Then, physicochemical and microbial stability tests of the formulation were conducted under long-term (12 months) and accelerated conditions (6 months). It was thus confirmed that both physicochemical and biological properties were stable during the test period. Consequently, an optimized formulation for the extract was developed and stability was confirmed.