Connectionist Temporal Classification (CTC) loss is commonly used in sequence learning applications. For example, in Automatic Speech Recognition (ASR) task, the training data consists of pairs of audio (input sequence) and text (output label),without temporal alignment information. Standard CTC computes a loss by aggregating over all possible alignment paths, that map the entire sequence to the entire label (full alignment). However, in practice, there are often cases where the label is incomplete. Specifically, we solve the partial alignment problem where the label only matches a middle part of the sequence. This paper proposes the wild-card CTC (W-CTC) to address this issue, by padding wild-cards at both ends of the labels. Consequently, the proposed W-CTC improves the standard CTC via aggregating over even more alignment paths. Evaluations on a number of tasks in speech and vision domains, show that the proposed W-CTC consistently outperforms the standard CTC by a large margin when label is incomplete. The effectiveness of the proposed method is further confirmed in an ablation study.