It has been well documented in many studies till now that patients in their first episode of psychosis demonstrate cognitive deficits. However, it is yet to be made clear how these deficits progress. Deterioration, stability or even amelioration in some domains has been noted from researchers. The aim of this study was to examine the longitudinal course of cognitive deficits over time. We administered a comprehensive battery of neuropsychological test to a group of first psychotic episode patients at the acute phase, 6 months and 1 year later. The sample comprised of 25 patients (13 male) in the first episode of psychosis. Specific tests of the Cambridge Neuropsychological Test Automated Battery (CANTAB) were used. The cognitive domains of attention, memory, working memory, visuospatial ability and planning, mental flexibility/shifting were examined. Repeated measures ANOVA was used in order to detect changes in the patients’ performance over time. According to our data, there was an improvement from baseline to 6 months in attention, planning and visual working memory. There was no change in performance in these cognitive domains from 6 months to 1 year from baseline. Memory, mental flexibility/shifting and visuospatial memory remained stable over time. Our data suggest variability concerning neuropsychological performance in specific tests examining different domains. Evaluation of cognitive function in the first episode of psychosis needs more thorough and comprehensive research, in relation to its course over time.