For male soccer players, the anthropometric profile and physical performance is already known but in women it is not well documented, the knowledge of these differences can qualify the training. Therefore, the aim of this study was two-fold: (i) to compare the anthropometric profile and physical fitness of Brazilian professional female and male soccer players; and (ii) analyze the relationships between anthropometric and physical fitness measures per sex. A cross-sectional study including 92 professional soccer players 44 women and 48 men was conducted. After one week of the end of the pre-season, the players from four different teams were assessed to anthropometric profile assessments and physical performance tests (e.g., jumping, linear sprint, change-of-direction and aerobic based test). Comparisons, correlation, and effect size analysis were performed between groups. Apart from the age and change-of-direction test, all other anthropometric and physical performance variables were significant different between women and men. Men were significantly faster than women in the 20 m linear sprint test (8.87%; p < .001; d = 2.382). The sum of skinfolds was correlated with some physical performance variables; however, body mass and body height were corrected with physical performance only for female soccer players. Thus, men performed better than women for most physical tests and presents differences in the anthropometric profile. Finally, coaches should consider that the anthropometric and performance profile are correlated differently between female and male soccer players. Thus, coaches should consider gender-specific parameters to create goals about the anthropometric and physical performance profile of players.