Ctenophryne aequatorialis (common name: Cuenca Nelson frog, reflecting its earlier placement in Nelsonophryne) is a species of frog in the family Microhylidae. It is endemic to the Andes of Ecuador and known from the Cuenca basin in Azuay Province southward to Saraguro Canton (northern Loja Province) at elevations of 2450m–2650mm (8,040feet–8,690feetm) asl.
Males measure about 27mm and females 37mm in snout–vent length. The dorsum has characteristic pattern of dark patches. The toes have basal webbing.
The species inhabits pastures, grassland, agricultural fields, and degraded secondary habitats. They have been collected close to small pools. Eggs are laid in small pools. The tadpoles reach metamorphosis after three months.
In Ecuador it is considered "endangered" because of its relatively small range, few known and presumably fragmented populations, and presumed decline in abundance. It might be present in the El Cajas National Park.