Advancements in neuroimaging, particularly diffusion MRI techniques and molecular imaging via PET, have significantly improved our ability to detect early biomarkers of both neurodegenerative and neuro-ophthalmic disorders, such as Alzheimer's, Parkinson's, multiple sclerosis (MS), neuromyelitis optica (NMO), and myelin oligodendrocyte glycoprotein (MOG) antibody disease. Despite these breakthroughs, the integration of AI-driven models has become crucial in harnessing the full potential of these technologies for clinical decision-making. This paper explores the role of advanced diffusion MRI techniques—specifically Neurite Orientation Dispersion and Density Imaging (NODDI) and Diffusion Kurtosis Imaging (DKI)—in revealing microstructural changes in brain and visual pathway tissues that precede clinical symptoms. These techniques, when paired with AI algorithms, enhance diagnostic precision, enabling the detection of early-stage degeneration and inflammatory processes with unprecedented accuracy. Additionally, the emergence of next-generation PET tracers targeting misfolded proteins, such as tau and alpha-synuclein, and inflammatory markers, further augments our ability to visualize and quantify pathological processes in vivo. The integration of AI, particularly deep learning models like convolutional neural networks (CNNs) and multimodal transformers, has demonstrated remarkable success in improving diagnostic accuracy, combining data from multiple imaging modalities, and providing predictive insights into disease progression. This review also examines the challenges associated with integrating AI into clinical practice, including technical variability, data privacy concerns, and regulatory hurdles. While these technologies promise to revolutionize early diagnosis and personalized treatment approaches, significant efforts in model validation, standardization, and clinical implementation remain crucial. The ongoing development of AI-enhanced neuroimaging holds great potential for advancing the precision of diagnosis and the effectiveness of therapeutic interventions in both neurodegenerative and neuro-ophthalmic disorders.