Background Severe fatigue may persist for many years in cancer survivors and has a considerable impact on a patient's life. This condition is called cancer-related fatigue (CRF). Mindfulness-Based Cognitive Therapy has shown to significantly reduce CRF in cancer survivors. Internet-delivered interventions can be valuable for fatigued patients who are not able to travel to a healthcare institute because of the lack of energy and/or physical limitations. Therefore, we have developed a web-based, therapist guided individual 9-week Mindfulness-Based Cognitive Therapy (eMBCT) aimed at diminishing CRF. Objective The aim of this study was to evaluate the efficacy of eMBCT in a clinical setting in reducing fatigue severity and distress in cancer survivors. Methods This pilot study was based on data from severely fatigued cancer survivors who applied for eMBCT between 2009 and 2013. Our primary outcome measure was the change in self-reported web-assessed fatigue severity, measured with the Fatigue severity subscale of the Checklist Individual Strength before (baseline) and one month after (post-assessment) eMBCT. The secondary outcome was distress (HADS) and the proportion of participants that showed clinically relevant improvement on fatigue severity. Patients' satisfaction with using eMBCT and reasons for non-adherence were studied. Intention-to-treat analyses were performed using multiple imputations to deal with data loss at post-assessment. All patients had to be severely fatigued at baseline (≥ 35 on the fatigue severity subscale of the Checklist Individual Strength), were > 18 years old, had no history of psychosis or current Major Depressive Disorder, finished their last cancer treatment at least six months ago (mixed cancer types), and were not in the terminal phase of illness. Patients were recruited offline as well as online. Results Two-hundred fifty-seven patients (age range 22–79 (M = 50.2, SD = 10.7), 76% women, 44% breast cancer, most had had surgery, chemo- and/or radiotherapy) met our inclusion criteria. Paired samples t-tests showed that fatigue severity was significantly reduced post-assessment (t(18) = 13.27, p < .001, Cohen's d: 1.45 as well as distress (t(46) = 7.66, p < .001, Cohen's d: 0.71). Thirty-five percent (n = 89) was clinically relevant improved at post-assessment and 62% (n = 159) adhered to treatment. This study had a completion rate of 1.5 and a registration rate of 2.3. Conclusion These findings suggest that individual eMBCT may be effective in reducing fatigue in cancer survivors. A randomized controlled study with a large sample and longer follow up is needed to demonstrate the effectiveness of eMBCT for CRF.