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Ketogenic low-carbohydrate high-fat (LCHF) diets are increasingly popular in broad sections of the population. The main objective of this study was to evaluate the effects of a non-energy-restricted ketogenic LCHF diet on muscle fatigue in healthy, young, and normal-weight women. Twenty-four women were randomly allocated to a 4-week ketogenic LCHF diet followed by a 4-week control diet (a National Food Agency recommended diet), or the reverse sequence due to the crossover design. Treatment periods were separated by a 15 week washout period. Seventeen women completed the study and were included in the analyses. Treatment effects were evaluated using mixed models. The ketogenic LCHF diet had no effect on grip strength or time to fatigue, measured with handgrip test (day 24–26). However, cycling time to fatigue decreased with almost two minutes (−1.85 min 95% CI:[−2.30;−1.40]; p < 0.001) during incremental cycling (day 25–27), accommodated with higher ratings of perceived exertion using the Borg scale (p < 0.01). Participants’ own diary notes revealed experiences of muscle fatigue during daily life activities, as well as during exercise. We conclude that in young and healthy women, a ketogenic LCHF diet has an unfavorable effect on muscle fatigue and might affect perceived exertion during daily life activities.