A new species of the genus Cnemaspis Strauch, 1887 is described from the Rajgad fort in the northern Western Ghats of Maharashtra, India. The new species, belonging to the flaviventralis clade, is one of the smallest known Indian Cnemaspis and can be distinguished from other congeners by its genetic distinctiveness and few key morphological characters. The new species can be diagnosed from all other Indian congeners by its small body size (SVL < 27 mm), the absence of conical and spine-like tubercles on flank; heterogeneous dorsal pholidosis; presence of only femoral pores and no precloacal pores in males; weakly keeled scales on the ventral surface of neck, pectoral, abdominal region and limbs; granular scales on the tail with whorls of slightly enlarged, strongly keeled tubercles; and the absence of enlarged median subcaudal scales. The new species is currently known to inhabit the man-made historical structures from a single locality in Rajgad, Maharashtra, where it is presumed to be uncommon.