The quasi-two-dimensional magnetic topological insulator MnBi$_2$Se$_4$, stabilized via non-equilibrium molecular beam epitaxy, is investigated by resonant soft x-ray scattering. Kiessig fringes are observed, confirming a high sample quality and a thin film thickness of 10 septuple layers ($\sim$13 nm). An antiferromagnetic Bragg peak is observed at the structurally forbidden reflection, whose magnetic nature is validated by studying its temperature, energy, and polarization dependence. Through a detailed analysis, an A-type antiferromagetic order with in-plane moments is implied. This alternative spin structure in MnBi$_2$Se$_4$, in contrast to the Ising antiferromagnetic states in other magnetic topological insulators, might be relevant for hosting new topological states.
