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Estimating the individual treatment effect (ITE) from observational data is meaningful and practical in healthcare. Existing work mainly relies on the strong ignorability assumption that no hidden confounders exist, which may lead to bias in estimating causal effects. Some studies consider the hidden confounders are designed for static environment and not easily adaptable to a dynamic setting. In fact, most observational data (e.g., electronic medical records) is naturally dynamic and consists of sequential information. In this paper, we propose Deep Sequential Weighting (DSW) for estimating ITE with time-varying confounders. Specifically, DSW infers the hidden confounders by incorporating the current treatment assignments and historical information using a deep recurrent weighting neural network. The learned representations of hidden confounders combined with current observed data are leveraged for potential outcome and treatment predictions. We compute the time-varying inverse probabilities of treatment for re-weighting the population. We conduct comprehensive comparison experiments on fully-synthetic, semi-synthetic and real-world datasets to evaluate the performance of our model and baselines. Results demonstrate that our model can generate unbiased and accurate treatment effect by conditioning both time-varying observed and hidden confounders, paving the way for personalized medicine.