We systematically study how the integrality of the conformal characters shapes the space of fermionic rational conformal field theories in two dimensions. The integrality suggests that conformal characters on torus with a given choice of spin structures should be invariant under a principal congruence subgroup of PSL(2, ℤ). The invariance strongly constrains the possible values of the central charge as well as the conformal weights in both Neveu-Schwarz and Ramond sectors, which improves the conventional holomorphic modular bootstrap method in a significant manner. This allows us to make much progress on the classification of fermionic rational conformal field theories with the number of independent characters less than five.