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Aim: The aim of this study was to systematically assess the risk of bias in osteosarcoma and Ewing’s sarcoma (ES) randomized controlled trials (RCT) and to examine the relationships between bias and conflict of interest/industry sponsorship. Methods: An OVID-MEDLINE search was performed (1976–2019). Using the Cochrane Collaboration guidelines, two reviewers independently assessed the prevalence of risk of bias in different RCT design domains. The relationship between conflicts of interest and industry funding with the frequency of bias was examined. Results: 73 RCTs met inclusion criteria. Prevalence of low-risk bias domains was 47.3%, unclear-risk domains 47.8%, and 4.9% of the domains had a high-risk of bias. Domains with the highest risk of bias were blinding of participants/personnel and outcome assessors, followed by randomization and allocation concealment. Overtime, frequency of unclear-risk of bias domains decreased (χ2 = 5.32, p = 0.02), whilst low and high-risk domains increased (χ2 = 8.13, p = 0.004). Studies with conflicts of interest and industry sponsorships were 4.2 and 3.1 times more likely to have design domains with a high-risk of bias (p < 0.05). Conclusion: This study demonstrates that sources of potential bias are prevalent in both osteosarcoma and ES RCTs. Studies with financial conflicts of interest and industry sponsors were significantly more likely to have domains with a high-risk of bias. Improvements in reporting and adherence to proper methodology will reduce the risk of bias and improve the validity of the results of RCTs in osteosarcoma and ES.