Affective brain-computer interfaces based on electroencephalography (EEG) is an important branch in the field of affective computing. However, individual differences and noisy labels seriously limit the effectiveness and generalizability of EEG-based emotion recognition models. In this paper, we propose a novel transfer learning framework with Prototypical Representation based Pairwise Learning (PR-PL) to learn discriminative and generalized prototypical representations for emotion revealing across individuals and formulate emotion recognition as pairwise learning for alleviating the reliance on precise label information. Extensive experiments are conducted on two benchmark databases under four cross-validation evaluation protocols (cross-subject cross-session, cross-subject within-session, within-subject cross-session, and within-subject within-session). The experimental results demonstrate the superiority of the proposed PR-PL against the state-of-the-arts under all four evaluation protocols, which shows the effectiveness and generalizability of PR-PL in dealing with the ambiguity of EEG responses in affective studies. The source code is available at https://github.com/KAZABANA/PR-PL.