In contrast to the findings of progressive structural brain changes in adolescence, longitudinal studies of patients with early onset schizophrenia spectrum disorders (EOS) indicate that neurocognitive deficits are relatively stable over the first years. The aim of this study is to assess neurocognitive functions longitudinally in patients with EOS compared to healthy controls (HC) using the MATRICS Cognitive Consensus Battery (MCCB). Methods Twenty patients with EOS and 41 HC were tested with the MCCB at baseline (T1) and after one (T2) and two years (T3). The mean age for the EOS group was 15.6 (SD=1.8) years, while the mean duration of illness was 1.7 (SD=1.4) years at T1. Results The EOS group's neurocognitive performances indicate a stable deficit on most measures. Both the EOS and HC groups showed improved neurocognitive functioning over time on all measures except for the verbal learning domain. There was an interaction between the EOS and HC groups' performance over time on the Trail Making Test A (TMA), a subtest on the processing speed domain. Conclusion The longitudinal neurocognitive performances measured by the MCCB confirm previous findings of stable deficits in patients with EOS. It is premature to conclude whether the increases in neurocognitive performance reflect developmental processes in adolescence or may be explained by learning effects, or both. As opposed to the other tests in this domain, a stagnation in processing speed as measured by the TMA suggests that the TMA is a particularly sensitive measure of neurodevelopmental deviance in EOS.