A junction between two boundaries of a topological superconductor (TSC), mediated by localized edge modes of Majorana fermions, is investigated. The tunneling of fermions across the junction depends on the magnetic flux. It breaks the time-reversal symmetry at the boundary of the sample. The persistent current is determined by the emergence of Majorana edge modes. The structure of the edge modes depends on the magnitude of the tunneling amplitude across the junction. It is shown that there are two different regimes, which correspond to strong and weak tunneling of Majorana fermions, distinctive in the persistent current behavior. In a strong tunneling regime, the fermion parity of edge modes is not conserved and the persistent current is a $2pi$-periodic function of the magnetic flux. When the tunneling is weak the chiral Majorana states, which are propagating along the edges have the same fermion parity. They form a $4pi$-phase periodic persistent current along the boundaries. The regions in the space of parameters, which correspond to the emergence of $2pi$- and of $4pi$-harmonics, are numerically determined. The peculiarities in the persistent current behavior are studied.
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