AbstractLong‐COVID caused by SARS‐CoV‐2 infection has significant and increasing effects on human health worldwide. Although a unifying molecular or biological explanation is lacking, several pathophysiological mechanisms have been proposed. Involvement of mast cells—evolutionary old “multipurpose” innate immune cells—was reported recently in studies of acute infection and post‐acute‐COVID‐19 syndrome. Mast cell activity has been suggested in long‐COVID. In this case–control study, we compared data from 24 individuals with long‐COVID (according to the NICE criteria) and 24 age‐ and sex‐matched healthy individuals with a history of SARS‐CoV‐2 infection without developing sequelae. Serum levels of the proteases beta‐tryptase (TPSB2) and carboxypeptidase (CPA3), which are mast cell specific, were measured using immunoassays. The values were compared between the two groups and correlated to measures of physical exertional intolerance. TPSB2 and CPA3 levels were median (range) 26.9 (2.0–1000) and 5.8 (1.5–14.0) ng/mL, respectively, in the long‐COVID group. The corresponding values in the control group were 10.9 (2.0–1000) (p = 0.93) and 5.3 (3.5–12.9) ng/mL (p = 0.82). No significant correlations between TPSB2 or CPA3 levels and scores on the ten physical subscales of SF‐36, 3.1–3.10 were revealed. We found no significant differences in the levels of mast cell activation markers TPSB2 and CPA3 between the long‐COVID and control groups and no correlations with proxy markers of exercise intolerance. Mast cell activation does not appear to be part of long‐term pathogenesis of long‐COVID, at least in the majority of patients.