The neural-network (NN)-based state estimation issue of Markov jump systems (MJSs) subject to communication protocols and deception attacks is addressed in this article. For relieving communication burden and preventing possible data collisions, two types of scheduling protocols, namely: 1) the Round-Robin (RR) protocol and 2) weighted try-once-discard (WTOD) protocol, are applied, respectively, to coordinate the transmission sequence. In addition, considering that the communication channel may suffer from mode-dependent probabilistic deception attacks, a hidden Markov-like model is proposed to characterize the relationship between the malicious signal and system mode. Then, a novel adaptive neural state estimator is presented to reconstruct the system states. By taking the influence of deception attacks into performance analysis, sufficient conditions under two different scheduling protocols are derived, respectively, so as to ensure the ultimately boundedness of the estimate error. In the end, simulation results testify the correctness of the adaptive neural estimator design method proposed in this article.