This perspective paper explores the untapped potential of artificial intelligence (AI), particularly machine learning-based dimension reduction techniques in multimodal neuroimaging analysis of Long COVID fatigue. The complexity and high dimensionality of neuroimaging data from modalities such as positron emission tomography (PET) and magnetic resonance imaging (MRI) pose significant analytical challenges. Deep neural networks and other machine learning approaches offer powerful tools for managing this complexity and extracting meaningful patterns. The paper discusses current challenges in neuroimaging data analysis, reviews state-of-the-art AI approaches for dimension reduction and multimodal integration, and examines their potential applications in Long COVID research. Key areas of focus include the development of AI-based biomarkers, AI-informed treatment strategies, and personalized medicine approaches. The authors argue that AI-driven multimodal neuroimaging analysis represents a paradigm shift in studying complex brain disorders like Long COVID. While acknowledging technical and ethical challenges, the paper emphasizes the potential of these advanced techniques to uncover new insights into the condition, which might lead to improved diagnostic and therapeutic strategies for those affected by Long COVID fatigue. The broader implications for understanding and treating other complex neurological and psychiatric conditions are also discussed.