Background: Mongolia is a vast, sparsely populated country in central Asia. Its harsh climate and nomadic lifestyle make the population vulnerable to acute respiratory infections, particularly influenza. Evidence on the morbidity, mortality and socioeconomic impact of influenza in Mongolia is scarce; however, routine surveillance for influenza-like illness (ILI), severe acute respiratory infection (SARI) and laboratory-detected influenza is conducted. This paper describes the epidemiology of influenza and the estimated burden of influenza-associated illness in Mongolia in the five influenza seasons between 2013–2014 and 2017–2018. Methods: Demographic and laboratory data from 152 sentinel surveillance sites on all patients who met the case definitions of ILI and SARI between October 2013 and May 2018 were extracted and analysed as described in A Manual for Estimating Disease Burden Associated with Seasonal Influenza. Results: The estimated annual influenza-associated ILI and SARI rates, presented as ranges, were 1279–2798 and 81–666 cases per 100 000 population, respectively. Children aged <5 years accounted for 67% of all ILI cases and 79% of all SARI cases. The annual specimen positivity for influenza was highest (11–30% for ILI and 8–31% for SARI) for children aged 5–<15 years and children <2 years old, respectively. The annual mortality rate due to pneumonia and SARI was highest among children aged <2 years (15.8–54.0 per 100 000 population). Although the incidence of influenza-associated ILI and SARI was lowest for people aged >65 years, the mortality rate due to pneumonia and SARI (1.2–5.1 per 100 000) was higher than that for those aged 15–64 years. Conclusion: The estimated influenza-associated ILI and SARI incidence rates are high in Mongolia, and children, especially those aged <5 years, have the highest influenza-associated burden in Mongolia. These findings provide evidence for decision-makers in Mongolia to consider targeted influenza vaccination, particularly for children.