We study the dynamics of an atomic condensate loaded in two symmetric traps where one of the trap is coupled to a non-Markovian reservoir. The system is fully described by the quantum-Langevin equation subjecting to Ornstein–Uhlenbeck dissipation kernel. We consider Ohmic dissipation with Lorentzian cutoff in our calculation. In this model dissipation is induced by the reservoir fluctuation in agreement with the Fluctuation–Dissipation theorem. We use simple numerical method to calculate the non-Markovian population evolution of the system. We found that stronger dissipation and higher temperature significantly effecting the population evolution of the non-Markovian two-mode system. Surprising dynamics is observed when the tunneling between the traps was inhibited as the system reaches it equilibrium.