An animal shelter and food trough system houses animals in a shelter which can be opened for ventilation while also preventing buildup of feed and debris within the shelter. The system includes a structure having a roof and an open lateral side extending down from an edge of the roof. A trough is positioned to extend along the open lateral side laterally offset outside of the edge of the roof. A panel has an upper edge coupled to the structure. The panel is pivotable between an open position and a closed position. A lower edge of the panel extends to a position adjacent to or beyond a distal side of the trough relative to the structure when the panel is in the closed position.