The spin ladder system BaFe 2 Se 3 presents puzzling magnetic behaviors, such as a spin-glass-like phase below ∼50 K. In this paper, an exchange bias effect with a large vertical shift in the field-cooled hysteresis loop is observed below 50 K. We also evidence the existence of uncompensated spins by susceptibility, magnetic remanence, and hysteresis loop measurements. The thermoremanent and isothermoremanent magnetization curves evidence a two-dimensional diluted antiferromagnet (DAFF) nature. Moreover, a nanometer-sized layered structure is observed by scanning electron microscope (SEM) and confirmed by scanning transmission electron microscope (STEM) coupled with electron energy loss spectroscopy (EELS). The discovery of exchange bias in antiferromagnetic BaFe 2 Se 3 crystals adds a new dimension to the research of its superconducting and multiferroic properties.