Mental disorders and their functional impacts evolve dynamically over time. Neurocognition and clinical symptoms are commonly modelled as predictors of functioning, however, studies tend to rely on static variables and adult samples with chronic disorders, with limited research investigating change in these variables in young people with emerging mental disorders. These relationships were explored in a longitudinal clinical cohort of young people accessing early intervention mental health services in Australia, around three-quarters of whom presented with a mood disorder (N = 176, aged 12–30 at baseline). Bivariate latent change score models quantified associations between neurocognition (a latent variable of working memory, verbal memory, visuospatial memory, and cognitive flexibility), global clinical symptoms, and functioning (self- and clinician-rated) and their relative change over follow-up (median = 20 months). We found that longitudinal changes in functioning were coupled with changes in global clinical symptoms (β = −0.43, P < 0.001), such that improvement in functioning was related to improvement in clinical symptoms. Changes in neurocognition were not significantly associated with changes in functioning or clinical symptoms. Main findings were upheld in three sensitivity analyses restricting the sample to: (a) adults aged 18–30; (b) participants with 12–24 months of follow-up; and (c) participants without a psychotic disorder. Our findings show that global symptom reduction and functional improvement are related in young people with emerging mental disorders. More work is needed to determine the temporal precedence of change in these variables. Future studies should apply this methodology to intervention studies to untangle the causal dynamics between neurocognition, symptoms, and functioning.