Schizophrenia is a mental health condition that severely impacts well-being. Cognitive impairment is among its core features, often presenting well before the onset of overt psychosis, underscoring a critical need to study it in the psychosis proneness (clinical high risk; CHR) stage, to maximize the benefits of interventions and to improve clinical outcomes. However, given the heterogeneity of cognitive impairment in this population, a one-size-fits-all approach to therapeutic interventions would likely be insufficient. Thus, identifying cognitive subtypes in this population is crucial for tailored and successful therapeutic interventions. Here we identify, validate, and characterize cognitive subtypes in large CHR samples and delineate their baseline and longitudinal cognitive and functional trajectories. Using machine learning, we performed cluster analysis on cognitive measures in a large sample of CHR youth (n = 764), and demographically comparable controls (HC; n = 280) from the North American Prodrome Longitudinal Study (NAPLS) 2, and independently validated our findings with an equally large sample (NAPLS 3; n = 628 CHR, 84 HC). By utilizing several statistical approaches, we compared the clusters on cognition and functioning at baseline, and over 24 months of followup. We further delineate the conversion status within those clusters. Two main cognitive clusters were identified, "impaired" and "intact" across all cognitive domains in CHR compared to HC. Baseline differences between the cognitively intact cluster and HC were found in the verbal abilities and attention and working memory domains. Longitudinally, those in the cognitively impaired cluster group demonstrated an overall floor effect and did not deteriorate further over time. However, a "catch up" trajectory was observed in the attention and working memory domain. This group had higher instances of conversion overall, with these converters having significantly more non-affective psychotic disorder diagnosis versus bipolar disorder, than those with intact cognition. In the cognitively intact group, we observed differences in trajectory based on conversion status, where those who start with intact cognition and later convert demonstrate a sharp decline in attention and functioning. Functioning was significantly better in the cognitively intact than in the impaired group at baseline. Most of the cognitive trajectories demonstrate a positive relationship with functional ones. Our findings provide evidence for intact and impaired cognitive subtypes in youth at CHR, independent of conversion status. They further indicate that attention and working memory are important to distinguish between the CHR with intact cognition and controls. The cognitively intact CHR group becomes less attentive after conversion, while the cognitively impaired one demonstrates a catch up trajectory on both attention and working memory. Overall, early evaluation, covering several cognitive domains, is crucial for identifying trajectories of improvement and deterioration for the purpose of tailoring intervention for improving outcomes in individuals at CHR for psychosis.