We investigate electronic structure theoretically in strained GaN/AlN quantum dots (QDs) with wurtzite (WZ) crystal structure. The QD electron energy levels are calculated using the finite element method (FEM) in the framework of effective mass approximation (EMA). We analyze the influence of strain and polarization to the electron energy levels and calculate electron energy levels with different dot sizes. It is shown that the strain dependent deformation potential and piezoelectric potential increase the electron energy levels and split the degenerate states. The electron energy levels decreases rapidly with increasing QD height, which is partly due to the confinement energy reduction. However, the piezoelectric field makes a more significant contribution.