Abstract We analyze excited baryon states using a holographic dual of quantum chromodynamics that is defined on the basis of an intersecting D4/D8-brane system. Studies of baryons in this model have been made by regarding them as a topological soliton of a gauge theory on a five-dimensional curved spacetime. However, this allows one to obtain only a certain class of baryons. We attempt to present a framework such that a whole set of excited baryons can be treated in a systematic way. This is achieved by employing the original idea of Witten, which states that a baryon is described by a system composed of open strings emanating from a baryon vertex. We argue that this system can be formulated by an Atiyah–Drinfeld–Hitchin–Manin-type matrix model of Hashimoto–Iizuka–Yi together with an infinite tower of the open string massive modes. Using this setup, we work out the spectra of excited baryons and compare them with the experimental data. In particular, we derive a formula for the nucleon Regge trajectory assuming that the excited nucleons lying on the trajectory are characterized by the excitation of a single open string attached on the baryon vertex.