We propose a configuration of a magnetic microtrap which can be used as an interferometer for three-dimensionally trapped atoms. The interferometer is realized via a dynamic splitting potential that transforms from a single well into two separate wells and back. The ports of the interferometer are neighboring vibrational states in the single well potential. We present a one-dimensional model of this interferometer and compute the probability of unwanted vibrational excitations for a realistic magnetic potential. We optimize the speed of the splitting process in order suppress these excitations and conclude that such interferometer device should be feasible with currently available microtrap technique. 03.75.-b, 03.65.-w, 39.20.+q, 39.25.+k, 39.90.+d