Background In Sierra Leone, the National Emergency Medical Services (NEMS) was designed to facilitate maternal and under-five referrals. During the COVID-19 pandemic, health facilities were repurposed and mobility restrictions were introduced, and this might have negatively influenced access to care. Thus, we compared utilization, timeliness and outcomes of referrals between the pre-COVID-19 and COVID-19 periods. Methods This was a cohort study using routinely collected data by the NEMS. There were 65 weeks in the pre-COVID-19 period (week one of January 2019 to week three of March 2020) and 91 weeks in the COVID-19 period (week four of March 2020 to week four of December 2021). We compared weekly referrals and the duration from initiating the NEMS for a referral to the patient reaching the receiving facility (prehospital delay) using the Mann-Whitney U test. Chi-squared tests were used to compare the mode of transportation and referral outcomes. Results Compared to the pre-COVID-19 period, there was significant decrease during the COVID-19 period in the median number of weekly maternal referrals (277 to 205), under-five referrals (177 to 104) and transfers on NEMS ambulances (348 to 269). The prehospital delays increased during the COVID-19 period for both maternal (72 to 86 minutes) and under-five (75 to 90 minutes) referrals (p<0.001). The percentage of NEMS ambulance transfers for maternal referrals was similar in both periods (90%), but for under-five referrals this decreased between the pre-COVID-19 (72%) and COVID-19 (68%) periods. In both periods, maternal (98%) and under-five (96%) referrals were successfully admitted to the receiving facilities. Conclusions The performance of the NEMS system in terms of referrals reaching the receiving health facilities was maintained during the pandemic. However, there is a need to sustain the current performance of the NEMS system while making more efforts to increase utilization and reduce delays during outbreaks/pandemics.