An initial Raman study on the effects of intercalation for aprotic electrolyte-based electrochemical double-layer capacitors (EDLCs) is reported. In situ Raman microscopy is employed in the study of the electrochemical intercalation of tetraethylammonium (Et4N+) and tetrafluoroborate (BF4−) into and out of microcrystalline graphite. During cyclic voltammetry experiments, the insertion of Et4N+ into graphite for the negative electrode occurs at an onset potential of +1.0 V versus Li/Li+. For the positive electrode, BF4− was shown to intercalate above +4.3 V versus Li/Li+. The characteristic G-band doublet peak (E2g2(i) (1578 cm−1) and E2g2(b) (1600 cm−1)) showed that various staged compounds were formed in both cases and the return of the single G-band (1578 cm−1) demonstrates that intercalation was fully reversible. The disappearance of the D-band (1329 cm−1) in intercalated graphite is also noted and when the intercalant is removed a more intense D-band reappears, indicating possible lattice damage. For cation intercalation, such irreversible changes of the graphite structure are confirmed by scanning electron microscopy (SEM).