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Primary lung tumours are rare in paediatric patients. Mucoepidermoid carcinoma (MEC), typically low-grade and diagnostically straightforward, is the second most common tumour of the bronchus after carcinoid tumours. However, rare MEC may show divergent differentiation, be misdiagnosed as low-grade adenocarcinoma, not otherwise classified, and pose clinical challenges, especially when mastermind-like protein 2 (MAML2) gene arrangement is negative by fluorescence in situ hybridisation (FISH). Here, we report an MAML2 FISH-negative low-grade bronchial tumour in a juvenile patient that demonstrates both mucoepidermoid and acinar differentiation based on morphology and immunophenotype. Next-generation sequencing identified a CREB regulated transcription coactivator 3 (CRTC3::MAML2) fusion gene, located upstream of traditional translocation points and potentially undetectable by currently available FISH probes. This tumour appears to be a novel presentation of a bronchial tumour with dual mucoepidermoid and acinar differentiation, first described as mucoacinar carcinoma—a newly proposed subtype of MEC, originally described in the major salivary gland.