Background There is a scarcity of data concerning the prevalence and pattern of malocclusion and orthodontic treatment needs in Syrian refugee. In this study, extra and intra-oral features of malocclusion and the dental health component of the Index of Orthodontic Treatment Need (IOTN) were reported. Methods Examination of 606 Syrian children/adolescents refugees attending Zaatari clinic was carried out (males = 280, females = 326, mean age = 11.84 ± 2.1 years). Subjects not within the age limit, with a history of orthodontic treatment, or with craniofacial anomalies were excluded. Both extra and intra-oral features of malocclusion were assessed. Intra-oral features included inter- and intra-arch occlusal characteristics: crowding, spacing, crossbite, overjet, overbite, molar and canine relationship, incisor relationship, and centerline shift. In addition, the dental health component (DHC) of the Index of Orthodontic Treatment Need (IOTN) was recorded. Gender and age variations in malocclusion characteristics and IOTN grading were tested using chi-square and nonparametric tests respectively (P < 0.05). Results The prevalence of malocclusion was 83.8% (52.6% class I, 24.2% class II, 7% class III). The most common features of malocclusion were crowding (71.1%) followed by centerline shift (52.1%), increased overjet (36.1%), high vertical proportions (34%) and deep overbite (31.2%); there were significant gender and age differences for a number of occlusal traits. The prevalence of moderate to severe need for orthodontic treatment was 67.7%. Conclusions This study provides baseline data on the prevalence of malocclusion in Syrian refugee children/adolescents in Zaatari camp where data concerning oral health of this population are lacking. The prevalence of orthodontic treatment need was high warranting the need for a comprehensive interceptive orthodontic program to prevent increasing oral health problems in the future. This high burden of oral diseases has a negative financial impact on the hosting country which can be reduced through public health interventions and implementing community-based dental healthcare for this underprivileged population.