An eccentricity tolerant valve stem seal assembly includes an elastomeric seal having an upper metal retainer extending down and within an upper seal portion which has an inwardly directed sealing lip for contacting a valve stem. There are also a flexible middle and a lower seal portions. The lower seal portion is connected to a lower metal seal retainer that is disposed up to a lower edge of the middle seal portion. The flexible middle seal portion allows the upper seal portion to flex from an eccentric valve stem without losing the sealing function of the sealing lip. In cooperation with the above described structure, a separate cover may be in a tight tolerance fit with the lower seal retainer over top of the eccentricity tolerant valve stem seal, in order to limit axial displacement of the upper portion of the seal due to high manifold pressure.