Higher-order fuzzy decision-making methods have become powerful tools to support decision-makers in solving their problems effectively by reflecting uncertainty in calculations better than crisp sets in the last 3 decades. Fermatean fuzzy set proposed by Senapati and Yager, which can easily process uncertain information in decision making, pattern recognition, medical diagnosis et al., is extension of intuitionistic fuzzy set and Pythagorean fuzzy set by relaxing the restraint conditions of the support for degrees and support against degrees. In this paper, we focus on the similarity measures of Fermatean fuzzy sets. The definitions of the Fermatean fuzzy sets similarity measures and its weighted similarity measures on discrete and continuous universes are given in turn. Then, the basic properties of the presented similarity measures are discussed. Afterward, a decision-making process under the Fermatean fuzzy environment based on TOPSIS method is established, and a new method based on the proposed Fermatean fuzzy sets similarity measures is designed to solve the problems of medical diagnosis. Ultimately, an interpretative multi-criteria decision making example and two medical diagnosis examples are provided to demonstrate the viability and effectiveness of the proposed method. Through comparing the different methods in the multi-criteria decision making and the medical diagnosis application, it is found that the new method is as efficient as the other methods. These results illustrate that the proposed method is practical in dealing with the decision making problems and medical diagnosis problems.