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Recently discovered quantum emitters in two-dimensional (2D) materials have opened new perspectives of integrated photonic devices for quantum information. Most of these applications require the emitted photons to be indistinguishable, which has remained elusive in 2D materials. Here, we investigate two-photon interference of a quantum emitter generated in hexagonal boron nitride (hBN) using an electron beam. We measure the correlations of zero-phonon-line photons in a Hong-Ou-Mandel (HOM) interferometer under non-resonant excitation. We find that the emitted photons exhibit a partial indistinguishability of $0.44 \pm 0.11$ in a 3 ns time window, which corresponds to a corrected value of $0.56 \pm 0.11$ after accounting for imperfect emitter purity. The dependence of the HOM visibility on the width of the post-selection time window allows us to estimate the dephasing time of the emitter to be $\sim 1.5$ ns, about half the limit set by spontaneous emission. A visibility above 90 % is under reach using Purcell effect with up-to-date 2D material photonics.