Fragile X syndrome (FXS) is a significant cause of intellectual disability and autism, while Fragile X Premutation -Associated Conditions (FXPAC) are a significant cause of morbidity and mortality globally. This study assessed the level of knowledge and perceptions about FXS and FXPAC among doctors in Nigeria. It was a web-based, cross-sectional study conducted among a cohort of doctors in Nigeria. Socio-demographic profile, knowledge of FXS, perceptions about FXS, knowledge of FXPAC, experience of doctors, and suggested ways of improving knowledge and management of FXS were obtained. Data were analyzed using STATA 16.0. Chi-square and Fishers exact tests of association were used to determine the association between variables, with the significance level set at p < 0.05. A total of 274 doctors participated in the study. A significant proportion of respondents had limited knowledge about the clinical features of FXS. Nine of ten (90.0%) participants with good knowledge of FXS had good perceptions of FXS management. This was statistically significant (p < 0.001). There was a high nonresponse rate to what FXPAC is (164/274, 59.9%) among the respondents because of insufficient knowledge. Suboptimal knowledge of FXS which influenced perception was noted among doctors. More strategies should be considered to improve doctors knowledge and management of FXS and FXPAC in Nigeria.