The burden of pain in newborn infants has been investigated in numerous studies, but little is known about the appropriateness of the use of pain scales according to the specific type of pain or infant condition. This systematic review aimed to evaluate the reporting of neonatal pain scales in randomized trials. A systematic search up to March 2019 was performed in Embase, PubMed, PsycInfo, Cinahl, Cochrane Library, Scopus and Luxid. Randomized and quasi-randomized trials reporting neonatal pain scales were included. Screening of the studies for inclusion, data extraction and quality assessment were performed independently by two researchers. Out of 3718 trials found, 352 with 29137 infants and 22 published pain scales were included. Most studies (92%) concerned procedural pain, where the most frequently used pain scales were PIPP or PIPP-R (48%), followed by NIPS (23%). Although NIPS is validated only for acute pain, it was also the second most used scale for ongoing and postoperative pain (21%). Only in a third of the trials, blinding for those performing the pain assessment was described. In 55 studies (16%), pain scales that were used lacked validation for the specific neonatal population or type of pain. Six validated pain scales were used in 90% of all trials, though not always in the correct population or type of pain. Depending on the type of pain and population of infants included in a study, appropriate scales should be selected. The inappropriate use raises serious concerns about research ethics and use of resources.