Background: Liver compresses are commonly applied in complementary medicine during cancer treatment and are believed to have an energizing effect. We conducted a pilot study to investigate the influence of external application of yarrow liver compresses on the autonomous nervous system by analyzing the heart rate variability (HRV) in metastatic cancer patients undergoing radiation therapy and suffering from cancer-related fatigue (CRF). Methods: A randomized pilot trial was undertaken with patients suffering from CRF receiving palliative radiation therapy for bone or brain metastasis over 2 weeks. CRF patients were randomized into an intervention group receiving yarrow liver compresses and a control group receiving no external application. HRV was analyzed at the beginning (T1) and end (T2) period of the study during daytime (d) and nighttime (n) in both groups and quantified using time-, frequency-, and nonlinear dynamics domains. Results: A total of 39 patients were randomized between September 2017 and August 2019 and a total of 20 patients (10 per group) were available for analysis. For both groups, significant differences in HRV analyses were found in the comparison over the timeline between the first and second measurement (T1d→T2d) during daytime. Specifically, the intervention group showed decreased HRV and complexity of heart rate regulation, indicating increased sympathetic activity at time T2d, whereas the control group showed increased HRV and complexity of heart rate regulation, indicating increased vagal activity at time T2d. Furthermore, the observed HRV analyses showed almost no significant differences between the 2 groups in a direct comparison at the beginning and the end of the study (exception: T2d). Conclusions: Yarrow liver compresses led to increased sympathetic activity during daytime in the intervention group, whereas in the control group, which did not receive any external application, increased parasympathetic activity was observed.