Abstract: The pass-through roof pipe seal system includes an adapter in the form of an inverted funnel with a vertical upper tube and integral lower flared skirt defining a central cavity through which a coolant pipe from a roof air-conditioning unit or the like passes. The pipe has an external layer of insulation around it except for a cut-away portion in the area of the funnel tube, which tube adheres directly and sealingly to the coolant pipe itself to prevent moisture from penetrating the system. The funnel skirt flares out over the lower edge of the cut-away portion of the invention and thus protects it from moisture and also overlies an inverted funnel-shaped vent cup having an upper vertical tube and lower skirt. The vent cup tube is adhered to the outside of the insulation layer around the coolant pipe below the adapter and is protected by the adapter skirt. The vent cup overlies the roof hole of a building upon which an air-conditioning unit is installed and prevents moisture from entering the building.