Abstract Embeddings of medical concepts such as medication, procedure and diagnosis codes in Electronic Medical Records (EMRs) are central to healthcare analytics. Previous work on medical concept embedding takes medical concepts and EMRs as words and documents respectively. Nevertheless, such models miss out the temporal nature of EMR data. On the one hand, two consecutive medical concepts do not indicate they are temporally close, but the correlations between them can be revealed by the time gap. On the other hand, the temporal scopes of medical concepts often vary greatly (e.g., common cold and diabetes). In this paper, we propose to incorporate the temporal information to embed medical codes. Based on the Continuous Bagof-Words model, we employ the attention mechanism to learn a “soft” time-aware context window for each medical concept. Experiments on public and proprietary datasets through clustering and nearest neighbour search tasks demonstrate the effectiveness of our model, showing that it outperforms five state-of-the-art baselines.