Kidney stones (Urolithiasis) are a common and recurrent urological disorder characterized by the formation of crystalline deposits in the kidneys, leading to pain, urinary complications, and potential renal damage. The limitations of conventional treatments, including recurrence and side effects, have increased the demand for safe and effective alternative therapies. This study evaluates the efficacy of a polyherbal capsule formulation in the management of kidney stones. The formulation includes Varuna (Crataeva nurvala), Keezhanelli (Phyllanthus niruri), Patharchatta (Bryophyllum pinnatum), Dandelion root (Taraxacum officinale), Ginger (Zingiber officinale), and Black cumin seeds (Nigella sativa), known for their anti-urolithiatic, diuretic, antioxidant, anti-inflammatory, and nephroprotective properties. Extracts were prepared using a preactivated Vedic extraction method to enhance bioavailability and stability. A pilot clinical study was conducted on 15 subjects with kidney stones (≤10 mm). The capsules were administered for 30–45 days, and parameters such as stone size, urinary markers, renal function, and symptom relief were assessed. Results showed a significant reduction in stone size, improvement in urinary and renal parameters, and relief from symptoms without any adverse effects. Animal studies further supported these findings by demonstrating reduced crystal deposition and improved kidney histology. Physico-chemical and microbial analyses confirmed the formulation’s safety and stability. The synergistic action of the herbs aids in stone dissolution, inhibition of crystal formation, increased urine output, and renal protection. In conclusion, the poly-herbal capsule formulation shows promising potential as a safe and effective natural therapy for kidney stone management. Further large-scale studies are recommended for validation.