Adipose tissue is a highly active endocrine organ that secrets many pro-inflammatory as well anti-inflammatory adipokines. The aim of the study was to assess serum adipokine profile in prepubertal vegetarian and omnivorous children. Sixty-two children on a vegetarian diet and fifty-five children on an omnivorous diet, aged 5 to 10 years, were studied. Dietary assessment was performed using a nutritional software program. Body composition was measured by dual-energy X-ray absorptiometry. Serum concentrations of adipokines: leptin, soluble leptin receptor (sOB-R), adiponectin (total and high molecular weight), resistin, visfatin, vaspin, and omentin were determined by immunoenzymatic assays. Both studied groups of children were comparable in terms of age, weight, height, body mass index, and body composition. Vegetarians had a lower (p = 0.017) leptin/sOB-R ratio and lower serum concentrations of resistin (p = 0.051), compared with omnivores. Average levels of other adipokines did not differ between both groups of children. However, we observed significantly higher ratios of anti-inflammatory to pro-inflammatory adipokines: adiponectin/leptin 0.70 (0.37–0.93) vs 0.39 (0.28–0.74), p = 0.005, and omentin/leptin 0.40 (0.23–0.83) vs. 0.33 (0.15–0.48), p = 0.011 in vegetarians compared with omnivores. A well-planned vegetarian diet might beneficially affect the adipokine profile and inflammatory status expressed by the ratios of anti-inflammatory to pro-inflammatory adipokines in prepubertal children.