We describe a distinct new rupicolous Cnemaspis based on four adult specimens collected from the Kedareshwar caves on Harishchandragad mountain, from the northern Western Ghats, approximately 1200 m asl. in Ahmednagar district of Maharashtra state, India. Cnemaspis uttaraghati sp. nov. can be diagnosed from all other peninsular Indian congeners by its small body size (maximum SVL < 39 mm), heterogeneous dorsal pholidosis, presence of spine-like tubercles on flanks; presence of only femoral pores in males; tail with enlarged, strongly keeled, conical tubercles forming whorls; median row of sub-caudal scales smooth, slightly enlarged, regularly arranged with condition of two slightly larger scales alternating with a large divided scale. The new species is likely to be allied to the C. girii clade and can be diagnosed from its members by its slightly larger body size, presence of spine-like tubercles on flanks, the number of enlarged tubercles in paravertebral rows between forelimb and hindlimb insertions, the number of dorsal tubercle rows at mid-body, the number of ventral scales across belly at mid-body, the number of longitudinal ventral scales from mental to cloaca, and the number of lamellae under digit IV of manus. We also provide a detailed morphological dataset for C. goaensis and C. indraneildasii based on topotypic material and specimens collected from additional localities to confirm C. indraneildasii is a junior synonym of C. goaensis, and provide an updated diagnosis for C. goaensis.