We report the equilibrium vortex phase diagram of a rotating two-band Fermi gas confined to a cylindrically symmetric parabolic trapping potential, using the recently developed finite-temperature effective field theory (Klimin et al 2016 Phys. Rev. A 94 023620). A non-monotonic resonant dependence of the free energy as a function of the temperature and the rotation frequency is revealed for a two-band superfluid. We particularly focus on novel features that appear as a result of interband interactions and can be experimentally resolved. The resonant dependence of the free energy is directly manifested in vortex phase diagrams, where areas of stability for both integer and fractional vortex states are found. The study embraces the BCS-BEC crossover regime and the entire temperature range below the critical temperature T c . Significantly different behavior of vortex matter as a function of the interband coupling is revealed in the BCS and BEC regimes. regime has also attracted much attention [27]. Vortex states in multiband quantum atomic gases have been studied to a far lesser extent.Therefore, in this work, the subject of our interest are fractional vortices in two-band Fermi gases of ultracold atoms in the BCS-BEC crossover. Although there is some similarity between superconductors and condensed atomic Fermi gases, the analogy is not complete. For one difference, cold gases certainly require an independent treatment by specific methods suitable in the entire BCS-BEC crossover range.Recently, the stability of different vortex states in a rotating trapped one-band Fermi gas has been theoretically studied in [14,15] using, respectively, the coarse-grained Bogoliubov-de Gennes (BdG) theory [28] (first applied to atomic Fermi gases in [29]) and the recently developed finite-temperature effective field theory (EFT) [30,31]. The finite-temperature EFT results agree with the results of the BdG theory and experiment for different manifestations: collective excitations and vortices [15,31], and solitons [32,33]. The finitetemperature EFT is aimed to find analytic results whenever possible. For example, for dark solitons in condensed Fermi gases, the finite-temperature EFT provides exact analytic solutions of the soliton equation of motion [32], while the BdG equations for the same problem have been solved only numerically.Besides our studies, there are several modifications of the EFT of condensed Fermi gases described in different publications and related to different ranges of external parameters (e.g., temperature and scattering length). They are developed either for the close vicinity to the critical temperature [34] or for the case T=0 (e.g., [35][36][37]). As analyzed in [31], the present finite-temperature EFT agrees with preceding works in all these limiting cases.At present, experimental data on vortices in two-band superfluid atomic Fermi gases are still lacking, in spite of the expected new physics stemming from the interband interactions in such a system. We report the first such theoretical study, to pave ...