The N-radial Schrödinger equation is analytically solved at finite temperature. The analytic exact iteration method (AEIM) is employed to obtain the energy eigenvalues and wave functions for all states n and l. The application of present results to the calculation of charmonium and bottomonium masses at finite temperature is also presented. The behavior of the charmonium and bottomonium masses is in qualitative agreement with other theoretical methods. We conclude that the solution of the Schrödinger equation plays an important role at finite temperature that the analysis of the quarkonium states gives a key input to quark-gluon plasma diagnostics.