By means of the first-principles calculations and magnetic topological quantum chemistry, we demonstrate that the low energy physics in the checkerboard antiferromagnetic (AFM) monolayer FeSe, very close to an AFM topological insulator that hosts robust edge states, can be well captured by a double-degenerate fragile topologically flat band just below the Fermi level. The Wilson loop calculations identify that such fragile topology is protected by the $S_{4z}$ symmetry, which gives rise to an AFM higher-order topological insulator that support the bound state with fractional charge $e/2$ at the sample corner. This is the first reported $S_{4z}$-protected fragile topological material, which provides a new platform to study the intriguing properties of magnetic fragile topological electronic states. Previous observations of the edge states and bound states in checkerboard AFM monolayer FeSe can also be well understood in our work.
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