Experimental evidence suggests that the Stokes shift may be considerable in silicon clusters. Multiple theoretical methods have been used to study this problem, with varying results: predicted Stokes shifts can differ in energy by several electron volts, and predicted minimum-energy structures can have either relaxed cores or relaxed outer shells. Here we present the lowest energy configuration for excited states and the Stokes shift for a series of silicon clusters in two separate ways. First, by energy minimization using density functional theory and changing the electronic occupation such that an electron is moved from the highest occupied molecular orbital to the lowest unoccupied molecular orbital; and second, by total-energy minimization using time-dependent density functional theory to calculate the energy of the first electronic transition with non-negligible oscillatory strength.