In this paper we propose an end-toend neural CRF autoencoder (NCRF-AE) model for semi-supervised learning of sequential structured prediction problems. Our NCRF-AE consists of two parts an encoder which is a CRF model enhanced by deep neural networks, and a decoder which is a generative model trying to reconstruct the input. Our model has a unified structure with different loss functions for labeled and unlabeled data with shared parameters. We developed a variation of the EM algorithm for optimizing both the encoder and the decoder simultaneously by decoupling their parameters. Our experimental results over the Part-of-Speech (POS) tagging task on eight different languages, show that the NCRF-AE model can outperform competitive systems in both supervised and semi-supervised scenarios.