Frequent resulting disability and case mortality support the urgency of investigation of the immune response mechanisms triggered by severe injury (SI) in children. This study aimed to determine the informative immunological criteria of traumatic injury severity and prognosis in children (n = 43) based on the assessment of expression of CD39 and CD73 ectonucleotidase in populations of regulatory T cells (Treg, CD4+CD127lowCD25high) and T-helper 17 cells (Th17, CD4+CD161+CD3+) in SI cases grouped by the outcome (favorable (SIfav, n = 24), unfavorable (SIunfav, n = 17) and lethal (n = 2)). With the help of flow cytometry, we identified a pronounced decrease in the absolute number of Treg and Th17, as well as Treg and Th17 expressing CD39 and CD73, in the early post-traumatic period. In the SIfav and SIunfav groups the relative number of Treg and Th17 cells expressing CD39 differed significantly (p <0.05); it was substantially higher form the first to the third day post injury in the SIunfav group. The level of Treg CD39 (44.4%) is a premise for an unfavorable outcome in children surviving an SI. In fatality cases, we registered extremely low ectonucleotidase expression rates: CD39+Treg — 9.52% (9.52–13.75) and CD39+Th17 — 0.92% (0.74–1.1). In the SIunfav group, the intensity of fluorescence (FL) of CD39 on Treg cells in the early post-traumatic period was higher than seen in the SIfav group. The threshold value for the average fluorescence intensity (FL) of CD39 on Treg was 8.25 c.u. In fatality cases, the Treg CD39 FL values were extremely low: 3.95 c.u. (3.7–4.67). The results of the study indicate that in children, the expression of CD39 and CD73 in Treg and Th17 populations is significantly associated with the severity of injury and outcome of the traumatic disease.