Nucleation is a fundamental and general process at the initial stage of first order phase transition. Although various models based on the classical nucleation theory (CNT) have been proposed to explain the energetics and kinetics of nucleation, detailed understanding on nanoscales are still required. Here we focus on homogeneous bubble nucleation, in which evaluation of the size dependence of bubble free energy is the key issue. We propose application of a formula in stochastic thermodynamics, the Jarzynski’s equality, for data analysis of molecular dynamics (MD) simulation to evaluate the free energy of bubble nucleation. As a test case, we performed a series of MD simulations with Lennard-Jones (LJ) fluid system. By applying an external spherical force field to equilibrated LJ liquid, we evaluated the free energy change during bubble growth as the Jarzynski’s ensemble average of required works. A fairly smooth free energy curve was obtained as a function of bubble radius in metastable liquid of mildly negative pressure conditions.