Introduction Very little is known about the burden of childhood oral diseases in protracted humanitarian settings.Aim This study aimed to assess the prevalence of oral diseases in Syrian refugee children living in Lebanon and to investigate their relationship with the duration of displacement.Methods Data from Miles for Smiles programme for Syrian refugee schoolchildren in Bekaa/Lebanon were used (n = 823). A dental examination was performed to assess the presence of dental caries and abscess. A clinical form was used to collect data on the presence, intensity and duration of dental pain.Results The majority (90%) had dental caries, 57% had dental pain (of which 55% had moderate/severe pain and 38% had pain for more than a month) and 9% had dental abscess. After adjusting for age and gender, children in protracted displacement were significantly more likely to have a higher number of decayed teeth compared to their counterparts who had been displaced for less than five years (RR = 1.19; 95% CI = 1.09-1.29; P <0.001).Conclusions The burden of oral diseases in Syrian refugee children living in Lebanon was high, particularly among those living in a protracted situation. There is a need for evidence-based effective public health interventions to improve this population's oral health.