A hydrogen generator having double burners and a method of operating the samewhere the hydrogen generator includes a housing, a barrier wall to divide a space in the housing into a first chamber and a second chamber, a fuel reformer installed in the first chamber, a first burner installed in the first chamber to heat a fuel reformer, a shift reactor installed in the second chamber, a second burner mounted in the barrier wall to heat the shift reactor, and a first igniter and a second igniter respectively ignite the first burner and the second burner.