We present measurements of the small-scale (0.1<~ r <~ 1 Mpc/h) quasar two-point correlation function at z>2.9, for a flux-limited (i<21) sample of 15 binary quasars compiled by Hennawi et al. (2009). The amplitude of the small-scale clustering increases from z ~ 3 to z ~ 4. The small-scale clustering amplitude is comparable to or lower than power-law extrapolations (with slope gamma=2) from the large-scale correlation function of the i<20.2 quasar sample from the Sloan Digital Sky Survey. Using simple prescriptions relating quasars to dark matter halos, we model the observed small-scale clustering with halo occupation models. Reproducing the large-scale clustering amplitude requires that the active fraction of the black holes in the central galaxies of halos is near unity, but the level of small-scale clustering favors an active fraction of black holes in satellite galaxies 0.1 <~ f_s <~ 0.5 at z >~ 3.