Complex electronic phases in strongly correlated electron systems are manifested by broken symmetries in the low-energy electronic states. Some mysterious phases, however, exhibit intriguing energy gap opening without an apparent signature of symmetry breaking (e.g., high-T_C cuprates and heavy fermion superconductors). Here, we report an unconventional gap opening in a heterostructured, iron-based superconductor Sr₂VO₃FeAs across a phase transition at T ₀ ∼150 K. Using angle-resolved photoemission spectroscopy, we identify that a fully isotropic gap opens selectively on one of the Fermi surfaces with finite warping along the interlayer direction. This band selectivity is incompatible with conventional gap opening mechanisms associated with symmetry breaking. These findings, together with the unusual field-dependent magnetoresistance, suggest that the Kondo-type proximity coupling of itinerant Fe electrons to localized V spin plays a role in stabilizing the exotic phase, which may serve as a distinct precursor state for unconventional superconductivity.