A common capping agent for gold nanorods, Cetyl trimethylammonium bromide (CTAB), is particularly problematic for biological studies because of its cytotoxicity. Several procedures have been developed to remove the CTAB from the surface of the gold nanorods, but most are lengthy, involving many steps, and use expensive reagents. Here, we present a simple, one-pot method for the complete removal of CTAB from the surface of gold nanorods, so that particles can be more effectively utilized in biological in vivo studies. The procedure involves first adding sodium borohydride to remove the CTAB, quickly followed by a replacement ligand, such as mercaptoundecanoic acid (MUA). Both the CTAB removal and MUA replacement were monitored by FTIR, surface enhanced Raman spectroscopy (SERS) and X-Ray Photoelectron Spectroscopy (XPS) and compared to commercially available citrate-capped gold nanorods. The procedure presented herein is shown to be as effective at removing CTAB and replacing it with MUA as commercially available gold nanorod samples.