Internal solitary waves moving over uneven bottoms are analyzed based on the reductive perturbation method, in which the amplitude, slope and horizontal lengthscale of a topography on the bottom are of the orders of ε, ε^5/2 and ε^−3/2, respectively, where the small parameter ε is also a measure of the wave amplitude. A free surface condition is adopted at the top of the fluid layer. That condition contains two parameters, δ and Δ, the first of which concerns the discontinuity of the basic density between the outer layer and the inner one; the second concerns the discontinuity of the mean density between them. An amplitude equation for the disturbance of order ε decomposes into a Korteweg-de Vries (KdV) equation and a system of algebraic equations for a stationary disturbance around a topography on the bottom. Solitary waves moving over a localized hill are studied in a simple case where both the basic flow speed and the Brunt-Vaisalla frequency are constant over the fluid layer. For this case, the expression for the amplitude of the stationary disturbance contains singular points with respect to basic flow speed. These singularities correspond to the resonant conditions modified by the free surface condition. The advancing speeds of solitary waves are changed by the influence of bottom topography, in a case where the long internal waves propagate in the direction opposite to the basic flow, but their waveforms remain almost unchanged.