The computer-based CogState Research Battery (CSRB) proposes a test structure which follows MATRICS recommended cognitive domains but lacks direct comparison to pen and paper batteries in first-episode psychosis (FEP). The aim of this study was to compare performances obtained with the CSRB and a pen and paper battery in a historical cohort of FEP patients. Among patients entering an early intervention program between 2003 and 2014, separate cohorts completed the traditional pen and paper cognitive battery (n = 182) and the CSRB (n = 97). Composite z-scores were derived using normative data of matched controls (n = 64 pen and paper, n = 69 CSRB) and were compared between the two batteries for the 7 cognitive domains. The cohort tested using the CSRB performed better on the domains of processing speed, attention, visual memory, and verbal memory than the cohort tested using the pen and paper battery (all p < 0.001). Performance did not differ between the two types of batteries for the working memory, executive functions, and social cognition domains. Cognitive profiles identified in the two patient cohorts were similar, with verbal memory being the most impaired domain. Better performances on the CSRB may be primarily due to the minimal demand of the computerized tests on graphomotor abilities and reading speed compared to the pen and paper tests. Our investigation offers a better understanding on how the results obtained with computerized batteries may compare to earlier work done with traditional tests.