Stacking polymorphism is a common characteristic of van der Waals layered materials and can substantially modify their physical properties. Here, based on first-principles calculations combined with electron and phonon transport theories, we systematically investigate the thermodynamic stability, electronic structure, lattice dynamics, and thermoelectric performance of Sc${}_2$Si${}_2$Te${}_6$ with three high-symmetry stacking sequences, namely, AA, AB, and ABC. We find that the AA- and AB-stacked structures are nearly degenerate in energy with the experimentally reported ABC phase, and that the maximum sliding barrier among these stacking sequences is only about 10~meV/atom, thereby accounting for the stacking faults observed experimentally. These three stacking sequences exhibit distinct electronic structures, with the conduction-band minimum being highly sensitive to the stacking sequence. As a consequence, the conduction-band degeneracies are 12, 2, and 8 for the ABC, AA, and AB stackings, respectively, leading to markedly different electronic transport properties near the band edge. The lattice thermal conductivity is governed primarily by three-phonon scattering, whereas four-phonon scattering provides an additional reduction, particularly in the ABC stacking. Among the three structures, the AB stacking exhibits the lowest lattice thermal conductivity owing to its stronger three-phonon scattering and lower phonon group velocity. As a result, the maximum thermoelectric figure of merit, $ZT$, is achieved in the AB structure, followed closely by the ABC structure, whereas the AA structure shows a substantially reduced value. These results demonstrate that the stacking sequence exerts a non-negligible influence on the thermoelectric performance of Sc${}_2$Si${}_2$Te${}_6$.