In this work, we report a comparative study of junction activation in the CdTe/CdS solar cells using MgCl2 and CdCl2 as the Cl sources. The chloride loading over the CdTe film was controlled by taking same molar solutions of both salts. Attention was given to explore the elemental profiles of S, O, Cl, Mg, and Cu across the CdTe as well as at the junction. Sulfur diffusion into the bulk of CdTe and evidence of alloying at the junction was prominent in the case of devices activated with CdCl2 as seen from SIMS and EQE data. The device parameters such as V-oc, J(sc) and FF were comparable or slightly higher for devices activated with MgCl2, which is explained as due to less recombination losses, lower series resistance and higher carrier concentration at the back contact region. The dispersion in efficiency values were smaller for devices activated with MgCl2 indicating that recrystallization of the CdTe film and junction activation in presence of MgCl2 results in better spatial uniformity compared to that with CdCl2. The devices used in this study were fabricated in an all-close-spaced sublimation (CSS) process, where both CdS and CdTe were deposited by CSS.