We theoretically study the magnetic-flux dependence of the critical current in Josephson junction formed by two s-wave superconductors on a three-dimensional topological insulator. We focus on the regime where the magnetic flux perpendicular to the junction is smaller than the flux quantum. The Fraunhofer pattern is different from the conventional form, showing fast decrease near the zero flux and nonzero critical current at the single flux quantum. These features are attributed to the Majorana fermions emerging in the junction.