Polyunsaturated fatty acid (PUFA) metabolites play important roles in the modulation of vascular tone, heart rate variability (HRV), and cardiovascular diseases. This study was undertaken to examine the relationship between HRV and the plasma levels of essential acids. Methods: Highly trained cross-country skiers participated in the study (n = 19). Time-domain and frequency-domain HRV analyses were performed. The plasma levels of fatty acids were determined using gas–liquid chromatography. Results: Plasma eicosapentaenoic acid and docosahexaenoic acid were found to be negatively correlated with resting heart rate (HR) (p = 0.026). The plasma levels of alpha-linolenic acid (ALA) were positively associated with the relative value of high-frequency power (rs = 0.465, p = 0.045) and negatively correlated with the sympathovagal balance ratio (rs = −0.493, p = 0.032) and the absolute and relative values of low-frequency power (rs = −0.490, p = 0.028). The plasma levels of arachidonic acid (ARA) were positively associated with the relative value of high-frequency power (rs = 0.59, p = 0.006) and negatively correlated with the sympathovagal balance ratio (rs = −0.54, p = 0.017) and the relative values of low-frequency power (rs = −0.52, p = 0.022). No correlation was found between n6/n3 and HRV parameters except for HR and pNN50. Conclusions: n-3 PUFAs and ARA play an important role in the autonomic regulation of heart rate in highly trained skiers. Athletes with substantial deficiencies in plasma ALA and excess levels of ARA had increased sympathetic and decreased parasympathetic activity.