It is well known that locomotion-dominated navigation tasks may highly provoke cybersickness effects. Past research has proposed numerous approaches to tackle this issue based on offline considerations. In this work, a novel approach to mitigate cybersickness is presented based on online adaptive navigation. Considering the Proportional-Integral-Derivative (PID) control method, we proposed a mathematical model for online adaptive navigation parametrized with several parameters, taking as input the users’ electro-dermal activity (EDA), an efficient indicator to measure the cybersickness level, and providing as output adapted navigation accelerations. Therefore, minimizing the cybersickness level is regarded as an argument optimization problem: find the PID model parameters which can reduce the severity of cybersickness. User studies were organized to collect non-adapted navigation accelerations and the corresponding EDA signals. A deep neural network was then formulated to learn the correlation between EDA and navigation accelerations. The hyperparameters of the network were obtained through the Optuna open-source framework. To validate the performance of the optimized online adaptive navigation developed through the PID control, we performed an analysis in a simulated user study based on the pre-trained deep neural network. Results indicate a significant reduction of cybersickness in terms of EDA signal analysis and motion sickness dose value. This is a pioneering work which presented a systematic strategy for adaptive navigation settings from a theoretical point.