Abstract Patient Electronic Health Records (EHR) data consist of sequences of patient visits over time. Sequential prediction of patients’ future clinical events (e.g., diagnoses) from their historical EHR data is a core research task and motives a series of predictive models including deep learning. The existing research mainly adopts a classification framework, which treats the observed and unobserved events as positive and negative classes. However, this may not be true in real clinical setting considering the high rate of missed diagnoses and human errors. In this paper, we propose to formulate the clinical event prediction problem as an events recommendation problem. An end-toend pairwise-ranking based collaborative recurrent neural networks (PacRNN) is proposed to solve it, which firstly embeds patient clinical contexts with attention RNN, then uses Bayesian Personalized Ranking (BPR) regularized by disease cooccurrence to rank probabilities of patient-specific diseases, as well as uses point process to provide simultaneous prediction of the occurring time of these diagnoses. Experimental results on two real world EHR datasets demonstrate the robust performance, interpretability, and efficacy of PacRNN.