We perform a high precision measurement of the spectrum of the QCD flux tube in three-dimensional $SU(2)$ gauge theory at multiple lattice spacings. We compare the results at large $qbar{q}$ separations $R$ to the spectrum predicted by the effective string theory, including the leading order boundary term with a non-universal coefficient. We find qualitative agreement with the predictions from the leading order Nambu-Goto string theory down to small values of $R$, while, at the same time, observing the predicted splitting of the second excited state due to the boundary term. On fine lattices and at large $R$ we observe slight deviations from the EST predictions for the first excited state.