© 2016 Elsevier Inc.The formulation for zero mode of a Bose–Einstein condensate beyond the Bogoliubov approximation at zero temperature [Y. Nakamura et al., Phys. Rev. A 89 (2014) 013613] is extended to finite temperature. Both thermal and quantum fluctuations are considered in a manner consistent with a concept of spontaneous symmetry breakdown for a finite-size system. Therefore, we need a proper treatment of the zero mode operators, which invoke non-trivial enhancements in depletion condensate and thermodynamical quantities such as the specific heat. The enhancements are visible in the weak interaction case. Our approach reproduces the results of a homogeneous system in the Bogoliubov approximation in a large particle number limit.