Abstract Background This pilot trial aimed to investigate whether modified short-term fasting (mSTF) reduces the incidence of chemotherapy-induced toxicities and whether an initial ketogenic diet (KD) as fasting supportive diet reduces fasting-related discomfort and improves the compliance. Methods In this controlled cross-over trial, gynaecologic cancer patients undergoing chemotherapy with a minimum of 4 cycles fasted for 96 h during half of their chemotherapy cycles and consumed a normocaloric diet during the other chemotherapy cycles. The caloric intake during mSTF was restricted to 25% of each patient’s daily requirement. In addition, half of the patients should eat a 6-day normocaloric KD prior to each mSTF period to investigate a KD’s hunger-suppression effect. Chemotherapy-induced toxicities, fasting-related discomfort, body composition, quality of life, laboratory values, and compliance were assessed at each chemotherapy. Results Thirty patients aged 30–74 years (median 54 years) completed the study. During mSTF the frequency and severity score of stomatitis [− 0.16 ± 0.06; 95% CI -0.28 - (− 0.03); P = 0.013], headaches [− 1.80 ± 0.55; 95% CI -2.89 – (− 0.71); P = 0.002], weakness [− 1.99 ± 0.87; 95% CI -3.72 – (− 0.26); P = 0.024] and the total toxicities’ score were significantly reduced [− 10.36 ± 4.44; 95% CI -19.22 - (− 1.50); P = 0.023]. We also observed significantly fewer chemotherapy postponements post-mSTF, reflecting improved tolerance of chemotherapy [− 0.80 ± 0.37; 95% CI -1.53 – (− 0.06); P = 0.034]. A significant reduction in mean body weight by − 0.79 ± 1.47 kg during mSTF was not compensated and remained until study’s conclusion (P < 0.005). On average, Insulin [− 169.4 ± 44.1; 95% CI -257.1 – (− 81.8); P < 0.001] and Insulin-like growth factor 1 levels [− 33.3 ± 5.4; 95% CI -44.1 – (− 22.5); P < 0.001] dropped significantly during fasting. The KD as a fasting supportive diet neither reduced fasting-related discomfort nor improved compliance of our fasting regimen. Conclusion MSTF is safe and feasible in gynaecologic cancer patients. Our results indicate that mSTF during chemotherapy can reduce chemotherapy-induced toxicities and enhance the tolerance of chemotherapy. Larger clinical trials are required to recommend mSTF for cancer patients. Trial registration germanctr.de: DRKS00011610, registered 30 January, 2017.