We report the synthesis of 11-mercaptoundecanoic acid (11-MUA) and 16-mercaptohexadecanoic acid (16-MHA) protected Au-25 clusters with moderate yields (similar to 15%) using a NaBH4 purification strategy. UVvis spectroscopy, transmission electron microscopy (TEM), and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry were employed to study the entire process of the isolation of 11-MUA-protected Au-25 clusters from a polydisperse Au cluster solution. UVvis and TEM data clearly show the formation of a polydisperse mixture, which upon the addition of NaBH4 leads to the growth and precipitation of non-Au-25 clusters, leaving the Au-25 clusters behind. MALDI MS shows the molecular ion peak for the 11-MUA-protected Au-25 cluster. 11-MUA-protected Au-25 clusters in THF were purified by slowly increasing the pH of the solution, which leads to the complete deprotonation of carboxyl groups on the surface and eventually precipitation of Au-25 clusters. Further protonation of these clusters by acetic acid leads to their solubilization in THF. These results show that, owing to the inherent stability of Au-25 clusters, a NaBH4 purification strategy can be used to isolate Au-25 clusters with surface carboxylic acid functionalities from a polydisperse Au cluster solution.