In this paper, the compression of an isolated cell by two rigid indenters is analyzed. The neo-Hookean model is employed to characterize the hyperelastic behavior of biological cells. Owing to the greatly increased ratio between surface energy density and elastic modulus, surface energy plays important roles in the mechanical performance of biological cells. Using the dimensional analysis method and a finite element approach incorporating surface energy, we study the elastic compression of hyperelastic cells at finite deformation and give the explicit relations of contact radius and indent depth depending on compressive load. Our results reveal that surface energy obviously influences both the local deformation and the overall responses of hyperelastic cells at finite deformation. The obtained results are useful to determine the elastic properties of biological cells from indent-depth curves accurately.