In Hořava-Lifshitz gravity a scaling isotropic in space but anisotropic in spacetime, often called "anisotropic scaling," with the dynamical critical exponent z=3, lies at the base of its renormalizability. This scaling also leads to a novel mechanism of generating scale-invariant cosmological perturbations, solving the horizon problem without inflation. In this paper we propose a possible solution to the flatness problem, in which we assume that the initial condition of the Universe is set by a small instanton respecting the same scaling. We argue that the mechanism may be more general than the concrete model presented here. We rely simply on the deformed dispersion relations of the theory, and on equipartition of the various forms of energy at the starting point.