This study compared the neuropsychological performance of two post-stroke groups, one undergoing rehabilitation and the other not receiving any intervention, on the acute and chronic stroke phases, and explored sociodemographic and neurological variables associated with changes in performance over time. Sixty-three adults underwent neuropsychological assessment with the Cognitive Screening Instrument (TRIACOG) less than thirty days after having a stroke and were reassessed three to six months after stroke. Thirty-eight participants did not undertake rehabilitation and twenty-five did physiotherapy and/or speech therapy between the two time points. The frequency of cognitive deficits (between groups) and the range of cognitive assessment scores over time (between and within groups) were analyzed. There was a significant decrease in the frequency of neuropsychological deficits and improvement on neuropsychological assessment scores over time only in the group undergoing rehabilitation. Severity of the neurological condition, years of education and being in rehabilitation explained the longitudinal changes in several cognitive domains measured by TRIACOG. Engaging in rehabilitation within three to six months post-stroke is crucial for enhancing the recovery of neuropsychological deficits. Cognitive screening instruments like TRIACOG can be used by health professionals to identify stroke-related neuropsychological changes and plan interventions.