Accurate assessments of population sizes and trends are fundamental for effective species conservation, particularly for social and long-lived species in which low reproductive rates, aging demographic structure and Allee effects could interact to drive rapid population declines. In the parrots (Order Psittaciformes) these life history characteristics have combined with habitat loss and capture for the pet trade to lead to widespread endangerment, with over 40% of species classified under some level of threat. Here we report the results of a population survey of one such species, the Yellow-naped Amazon, Amazona auropalliata, that is classified as ‘Endangered’ on the IUCN Red List. We conducted a comprehensive survey in June and July of 2016 of 44 night roosts of the populations in contiguous Pacific lowlands of northern Costa Rica and southern Nicaragua and compared numbers in Costa Rica to those found in a similar survey conducted in June 2005. In 2016 we counted 990 birds across 25 sites surveyed in Costa Rica and 692 birds across 19 sites surveyed in Nicaragua for a total population estimate of only 1,682 birds. Comparisons of 13 sites surveyed in both 2005 and 2016 in Costa Rica showed a strong and statistically significant decline in population numbers over the 11-year period. Assessment of group sizes approaching or leaving roosts indicated that less than 25% of groups consisted of three or more birds; there was a significantly higher proportion of these putative family groups observed in Nicaragua than Costa Rica. Taken together, these results are cause for substantial concern for the health of this species in a region that has previously been considered its stronghold, and suggest that stronger conservation action should be undertaken to protect remaining populations from capture for the pet trade and loss of key habitat.