Deep Learning (DL) has become a popular technique in various domains to assist the human decisions, including games, news, finance, economy, biology, medicine and engineering. For clinical domain, even though statistical learning approaches have been used for clinical decision support for years, except the image related tasks, the application of deep learning mostly stays in the literature, not in the real practice. As the key component of clinical decision support system, clinical natural language processing (NLP) still relies on rule-based or statistical-based solutions while other domains have widely applied deep learning based approaches. In this paper, we provide a view on the challenges that deep learning will face for clinical NLP applications, and discuss the not yet funded opportunities from it. Overall, we want to show the broad picture about clinical NLP to deep learning researchers and encourage them to actively contribute to this field.