Introduction: Patients with chronic intestinal failure (IF) have a low degree of physical activity, decreased muscle mass, and decreased muscle strength, leading to a high risk of sarcopenia. We aimed to test the prevalence of sarcopenia by the use of SARC-F and EWGSOP and to investigate the association between the two at baseline and after 12 weeks of an exercise intervention. Methods: Thirty-one patients with chronic IF completed 12 weeks of three weekly home-based individualized exercise sessions. Body composition was measured by bioimpedance analysis and physical function by handgrip strength (HGS) and timed up-and-go (TUG). Sarcopenia was assessed by SARC-F and EWGSOP. Multiple regression analysis was used to test for the association between the two tools. Results: The prevalence of sarcopenia measured by EWGSOP was 59%. This prevalence did not change after the intervention. At baseline, 38.8% of patients were screened as at risk for sarcopenia by SARC-F. This decreased to 29.0% after the intervention (P < 0.001). A statistically significant increase was achieved in muscle mass (P = 0.017) and muscle mass index (P = 0.016). Furthermore, both TUG (P = 0.033) and HGS (P = 0.019) improved. Conclusions: Sarcopenia is prevalent in patients with chronic IF. EWGSOP finds more patients to be at risk of sarcopenia than SARC-F but was not sufficiently sensitive to measure changes induced by the physical intervention. The significant change in SARC-F may illustrate that patients, themselves, find an improvement in self-perceived health.