We demonstrate the efficacy of ion-pair chromatography for separations of samples of charged, polydisperse, water-soluble gold nanoparticles protected by monolayers of N-acetyl-L-cysteine and of tiopronin ligands. These nanoparticle mixtures have 1-2-nm-diameter Au core sizes as estimated from UV-visible spectra of the separated components. This size range encompasses the transition from bulk metal to molecular properties. The nanoparticle mixtures were resolved, the smallest nanoparticles eluting first, on an octadecylsilyl (C18) column using isocratic elution with a methanol/water mobile phase containing tetrabutylammonium fluoride (Bu4N+F-) and phosphate buffer. The column retention increases with Bu4N+F- concentration, lowered pH, and decreasing methanol volume fraction. The retention mechanism is dominated by ion-pairing in either the mobile phase or at the stationary/mobile-phase interface. Size exclusion effects, used in many previous nanoparticle separations, are insignificant.