The Physician Payments Sunshine Act requires disclosure of payments made by drug and medical device manufacturers to physicians or teaching hospitals. Academic literature extensively documents gender disparities in the medical profession with regard to salary, promotion, and government funded research. This investigation sought to quantify potential conflicts of interest (CoIs) in pediatric medical journals, specifically examining sex differences. To identify potential CoIs, we examined manuscripts published prior to 2019 in six pediatric journals (JAMA Pediatrics, Pediatrics, The Journal of Pediatrics, Pediatric Blood and Cancer, Pediatric Critical Care Medicine, and The Pediatric Infectious Disease Journal). We collected physician demographics and specialty from the National Plan and Provider Enumeration System National Provider Identifier Registry and compensation data from both ProPublicas Dollars for Docs (PDD) and Centers for Medicare and Medicaid Services Open Payments (CMSOP). Data was collected on 2,747 authors from 929 manuscripts. Of the 1,088 authors based in the United States with medical degrees (40.5% female), 510 (46.9%) had entries in PDD and CMSOP. Overall, 11,791 payments to these physician-authors totaled $9,586,089.97. Males were 19.6% more likely to receive payments (RR = 1.20, 95% CI [1.05, 1.37], p = 0.008). The mean amount received by males was $23,250.71 while that received by females was $10,970.78 (mean difference = 12,279.92, 95% CI = (2036.31, 22,523.54), p = 0.019). A comprehensive understanding of these CoIs can inform the disclosure policies of journals to promote transparency of authors.