Understanding and accurately estimating cognitive workload is crucial for the development of adaptive, user-centered interactive systems across a variety of domains including augmented reality, automotive driving assistance, and intelligent tutoring systems. Cognitive workload assessment enables dynamic system adaptation to improve user experience and safety. In this work, we introduce a novel framework that leverages smooth pursuit eye movements as a non-invasive and temporally precise indicator of mental effort. A key innovation of our approach is the development of trajectory-independent algorithms that address a significant limitation of existing methods, which generally rely on a predefined or known stimulus trajectory. Our framework leverages two solutions to provide accurate cognitive load estimation, without requiring knowledge of the exact target path, based on Kalman filter and B-spline heuristic classifiers. This enables the application of our methods in more naturalistic and unconstrained environments where stimulus trajectories may be unknown. We evaluated these algorithms against classical supervised machine learning models on a publicly available benchmark dataset featuring diverse pursuit trajectories and varying cognitive workload conditions. The results demonstrate competitive performance along with robustness across different task complexities and trajectory types. Moreover, our framework supports real-time inference, making it viable for continuous cognitive workload monitoring. To further enhance deployment feasibility, we propose a federated learning architecture, allowing privacy-preserving adaptation of …