Background: Stroke can result in cognitive complaints that can have a large impact on quality of life long after its occurrence. A number of computer-based training programs have been developed with the aim to improve cognitive functioning. Most studies investigating their efficacy used only objective outcome measures, whereas a reduction of subjective cognitive complaints may be equally important for improving quality of life. A few studies used subjective outcome measures but were inconclusive, partly due to methodological shortcomings such as lack of proper active and passive control groups. Objective: The aim of the current study was to investigate whether computer-based cognitive flexibility training can improve subjective cognitive functioning and quality of life after stroke. Methods: We performed a randomized controlled double blind trial (RCT). Adults (30–80 years old) who had a stroke 3 months to 5 years ago, were randomly assigned to either an intervention group (n = 38), an active control group (i.e., mock training; n = 35), or a waiting list control group (n = 24). The intervention and mock training consisted of 58 half-hour sessions within 12 weeks. The primary subjective outcome measures were cognitive functioning (Cognitive Failure Questionnaire), executive functioning (Dysexecutive Functioning Questionnaire), quality of life (Short Form Health Survey), instrumental activities of daily living (IADL; Lawton & Brody IADL scale), and participation in society (Utrecht Scale for Evaluation of Rehabilitation-Participation). Secondary subjective outcome measures were recovery after stroke, depressive symptoms (Hospital Anxiety Depression Scale—depression subscale), fatigue (Checklist Individual Strength—Fatigue subscale), and subjective cognitive improvement (exit list). Finally, a proxy of the participant rated the training effects in subjective cognitive functioning, subjective executive functioning, and IADL. Results and conclusions: All groups improved on the two measures of subjective cognitive functioning and subjective executive functioning, but not on the other measures. These cognitive and executive improvements remained stable 4 weeks after training completion. However, the intervention group did not improve more than the two control groups. This suggests that improvement was due to training-unspecific effects. The proxies did not report any improvements. We, therefore, conclude that the computer-based cognitive flexibility training did not improve subjective cognitive functioning or quality of life after stroke.