Introduction: The management of eruption disturbances in orthodontics may be challenging and requires a careful diagnosis and treatment planning. This case report discusses the challenges of a two-phase orthodontic treatment of a patient presenting with a dental eruption pattern anomaly. Patient concerns: A 10-year-old boy was presented with no complaints for a routine orthodontic evaluation during mixed dentition. Primary diagnoses: The patient was diagnosed with a skeletal Class I malocclusion with unilateral posterior crossbite, incomplete mandibular lateral incisor-canine transposition and a unilateral maxillary ectopic canine. Interventions: Phase 1 started with rapid maxillary expansion to correct maxillary constriction and the ectopic eruption of the right maxillary canine. In the mandibular arch, phase 1 included the extraction of the left primary lateral incisor and canine, alignment of the left permanent lateral incisor and orthodontic traction of the left permanent canine. The duration of phase 1 was 14 months. Phase 2 involved a comprehensive course of orthodontic treatment and started when the patient was aged 13 years. This phase lasted 18 months. Results: An adequate dental occlusion was obtained, and the treatment results were stable after an 18-month follow-up. Conclusion: In this case, the early diagnosis of the dental anomalies was valuable as it allowed an early intervention to be undertaken, which resulted in overall treatment simplification and potentially minimised the adverse effects. This case report reinforces the importance of a careful follow-up during mixed dentition.