In this study we propose a subject specific deep neural network (SSDNN) model for analyzing pharmacokinetic (PK) and pharmacodynamic (PD) data. PK and PD data are obtained at subject-specific irregular time intervals, and a different number of observations are collected for each subject, based on the number of times the subject visited the hospital. The SSDNN’s performance is compared to that of the standard neural network (NN) and support vector machine (SVM) using three evaluation metrics, which are mean squared error (MSE), mean absolute error (MAE) and mean relative absolute error (MRAE). We find that the absolute values of the four measures of the proposed SSDNN are significantly lower than those of NN and SVR for PK and PD data. These findings imply that the proposed SSDNN is an appealing tool for analyzing PK and PD data.