Steady-state visual evoked potential (SSVEP)-based brain-computer interfaces (BCIs) have emerged as a prominent technology due to their high information transfer rate, rapid calibration time, and robust signal-to-noise ratio. However, a critical challenge for practical applications is performance degradation caused by user fatigue during prolonged use. This work proposes novel methods to address this challenge by dynamically adjusting data acquisition length and updating detection models based on a fatigue-aware stopping strategy. Two 16-target SSVEP-BCIs were employed, one using low-frequency and the other using high-frequency stimulation. A self-recorded fatigue dataset from 24 subjects was utilized for extensive evaluation. A simulated online experiment demonstrated that the proposed methods outperform the conventional fixed stopping strategy in terms of classification accuracy, information transfer rate, and selection time, irrespective of stimulation frequency. These findings suggest that the proposed approach can significantly improve SSVEP-BCI performance under fatigue conditions, leading to superior performance during extended use.