This paper proposes a new method to determine earthquake magnitude for small deep-focus earthquakes by using velocity-amplitude data. For deep-focus earthquakes, body-wave magnitude has been widely used, but it is difficult to directly apply the conventional methods to the data from short-period seismometers of regional networks. In the proposed method, moment magnitude is used to obtain the attenuation function for epicentral distance and focal depth, where the influence of inhomogeneous Q structure is incorporated. This effect is further reduced by introducing a correction term that is a function of distance from the trench axis to an observation station and focal depth. The attenuation function and correction term were estimated for the velocity amplitude data obtained by the network of the Japan Meteorological Agency. The velocity-amplitude magnitude we propose is in satisfactory agreement with the moment magnitude, and provides stable magnitude values for small earthquakes of deep to shallow focal depths seamlessly.