Bioelectrical impedance analysis (BIA) and anthropometry are considered alternatives to well-established reference techniques for assessing body composition. In team sports, the percentage of fat mass (FM%) is one of the most informative parameters, and a wide range of predictive equations allow for its estimation through both BIA and anthropometry. Although it is not clear which of these two techniques is more accurate for estimating FM%, the choice of the predictive equation could be a determining factor. The present study aimed to examine the validity of BIA and anthropometry in estimating FM% with different predictive equations, using dual X-ray absorptiometry (DXA) as a reference, in a group of futsal players. A total of 67 high-level male futsal players (age 23.7 ± 5.4 years) underwent BIA, anthropometric measurements, and DXA scanning. Four generalized, four athletic, and two sport-specific predictive equations were used for estimating FM% from raw bioelectric and anthropometric parameters. DXA-derived FM% was used as a reference. BIA-based generalized equations overestimated FM% (ranging from 1.13 to 2.69%, p < 0.05), whereas anthropometry-based generalized equations underestimated FM% in the futsal players (ranging from −1.72 to −2.04%, p < 0.05). Compared to DXA, no mean bias (p > 0.05) was observed using the athletic and sport-specific equations. Sport-specific equations allowed for more accurate and precise FM% estimations than did athletic predictive equations, with no trend (ranging from r = −0.217 to 0.235, p > 0.05). Regardless of the instrument, the choice of the equation determines the validity in FM% prediction. In conclusion, BIA and anthropometry can be used interchangeably, allowing for valid FM% estimations, provided that athletic and sport-specific equations are applied.