The importance of fat mass estimation in multiple areas related to health and sports has led to the emergence of a large number of methods and formulas for its estimation. The aim of the present study was to compare the agreement and differences between different formulas for estimating fat mass by anthropometry. Eighty-seven subjects underwent an anthropometric assessment following the protocol from the International Society for the Advancement of Kinanthropometry (ISAK). The fat percentage was calculated with 14 different formulas for men and with 12 different formulas for women. In the case of men, they were proposed by Durnin-Womersley, Yuhasz, Faulkner, Carter, Peterson, Katch-McArdle, Sloan, Wilmore, Evans, Lean, Reilly, Civar, Hastuti, and Kerr. In the case of women, the equations used were those proposed by Durnin-Womersley, Yuhasz, Faulkner, Carter, Peterson, Katch-McArdle, Sloan, Wilmore, Evans, Lean, Thorland, and Kerr. Significant differences were found between the formulas in both men (8.90 ± 2.17% to 17.91 ± 2.84%; p < 0.001–0.016) and women (15.33 ± 2.94% to 28.79 ± 3.30%; p < 0.001–0.004). It was observed that in the case of men, the Carter and Yuhasz formulas and the Civar and Faulkner formulas showed moderate agreement with each other (CCC = 0.910–0.915). In the case of women, it was observed that the Carter and Yuhasz formulas showed moderate agreement with each other (CCC = 0.974). In conclusion, the formulas used for the estimation of lipid mass in anthropometry reported significantly different results between them and were therefore not comparable.