Cetyltrimethylammonium bromide (CTAB)-based surfactants are typically used as morphology-directing/stabilising agents for gold nanorods (AuNRs), forming bilayers on their surface. However, the biological applications of AuNRs require the removal of surface-bound CTAB due its high toxicity and the poor colloidal stability of CTAB-covered AuNRs in biological media. Herein, we report a simple and effective strategy for removing surface-bound cetyltrimethylammonium (CTA) cations from poly(ethylene glycol)thiolate-protected AuNRs (PEG-AuNRs) by treatment with dimethyl sulfoxide/citric acid (DMSO/Cit), achieving residual CTA ion levels that cannot be detected by highly sensitive mass spectrometry or X-ray photoelectron spectroscopy (XPS) techniques. The DMSO/Cit treatment is thought to destabilise the Ag–Br–CTA complex on AuNRs, since citric acid forms strongly bound chelate complexes with CTA cations.