Background: Global disruption of measles vaccination coverage during the COVID-19 pandemic may amplify the future prevalence of the fatal post-measles neurodegenerative disorder Subacute Sclerosing Panencephalitis (SSPE). To provide a foundation for future comparison, we assessed SSPE cases about their vaccination status prior to the COVID-19 pandemic, between March 1, 2019, and August 31, 2019. Methods: A 26-week prospective study of SSPE was performed at a tertiary care facility serving urban and rural regions of Peshawar in northern Pakistan and the adjacent region of Afghanistan. Results: Sixty-six cases of SSPE were diagnosed at a mean age of 6.67 years, including 38 measles-vaccinated, 19 unvaccinated, and 9 with unknown vaccination status. Only 57% of the patients had received the 1st dose of the measles vaccine, and, among them, only 38% had received the second dose. Interpretation: While the preventable disease SSPE is now rare in countries with effective vaccination campaigns targeting measles, vaccination coverage remains insufficient in Pakistan (and neighboring Afghanistan). Investigation into the causes of vaccine failure in Pakistan needs urgent attention. Directed community education, mandatory measles vaccination, proper registration of acute measles infection, and particularly of SSPE, are key factors that need to be addressed so this deadly disease can be controlled and prevented.