In arXiv:1104.2843, a microscopic top-down model of a holographic superconductor is constructed using two intersecting D8-branes in the bulk in D4-brane background. This is a non-BPS configuration which has tachyons in its spectrum signaling instability of the system. This instability has been proposed to be the bulk analogue of the BCS instability in the boundary theory in 1104.2843. Our aim is to study a similar simplified system at finite temperature and evaluate the transition temperature. We thus consider a system of two intersecting D3 -branes in flat background, we compute one-loop finite temperature correction to tachyon two-point amplitude and find, numerically, the transition temperature at which effective mass-squared of the tachyon becomes zero. We further extend the calculation of tachyon two-point amplitude to the case of intersecting stacks of D3-branes.