Quantum chemistry is one of the important applications of quantum information technology. Especially, an estimation of the energy gap between a ground state and excited state of a target Hamiltonian corresponding to a molecule is essential. In the previous approach, an energy of the ground state and that of the excited state are estimated separately, and the energy gap can be calculated from the subtraction between them. Here, we propose a direct estimation of the energy gap between the ground state and excited state of the target Hamiltonian with quantum annealing. The key idea is to combine a Ramsey type measurement with the quantum annealing. This provides an oscillating signal with a frequency of the energy gap, and a Fourier transform of the signal let us know the energy gap. Based on typical parameters of superconducting qubits, we numerically investigate the performance of our scheme when we estimate an energy gap between the ground state and first excited state of the Hamiltonian. We show robustness against non-adiabatic transitions between the ground state and first-excited state. Our results pave a new way to estimate the energy gap of the Hamiltonian for quantum chemistry.