The inertial navigation system/Doppler velocity logger (INS/DVL) plays an important role in ocean navigation. Any DVL malfunction poses serious risks to navigation. A precise detection system is required to detect the initial moments of DVL signal malfunctions; moreover, with loss of DVL, a fault-tolerant scheme (FTS) is necessary for DVL signal reconstruction. In this paper, an evolutionary knowledge-based method, namely improved evolutionary TS-fuzzy (I-eTS), is adopted to build an artificial intelligence (AI)-based pseudo DVL to deal with long-term outage of DVL. By employing Gaussian process regression (GPR) models for fault detection, a new FTS is constructed. To verify the effectiveness of the new fault detection and fault tolerance system, navigation data is gathered by a test setup and algorithms are performed in the laboratory. In the tests, it is demonstrated that the proposed FTS leads to rapid detection of both gradual and abrupt faults, which leads to less interaction between fault detection and FTS.