Rare neurodegenerative diseases are a diverse group of disorders characterized by progressive neuronal loss and considerable challenges in diagnosis and treatment. Recent advances in high-throughput omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have generated large molecular datasets that provide deeper insights into disease-associated mechanisms. However, integrating heterogeneous omics datasets and extracting biologically meaningful patterns remains challenging. Specifically, the modernized machine learning architectures, such as deep neural networks, random forests, and graph-based computational models, are applied to decipher complex non-linear interactions across high-dimensional multi-omics datasets. By synthesizing multi-omics platforms with the layered biological information, AI-driven pipelines enhance the phenotypic profiling,early diagnostic classification, and streamline the discovery of targetable disease networks in rare neurodegenerative diseases. Furthermore, machine learning also supports the computational drug repurposing and candidate screening and accelerate the therapeutic development where the traditional clinical trials are are limited. Despite these technological strides, key bottleneck challenges persist, such as limited training sample sizes, data sparsity, missing multi-omics profiles, batch effects, and the need for complex model interpretation in clinical translations. These can be addressed through robust cross-validation, explainable AI, and international collaborative data training. Machine learning with multi-omics datasets with bioinformatics provides a transformative paradigm towards the precision medication and targeted disease-modifying therapies for patients. This chapter discusses the role of artificial intelligence (AI) and machine learning in supporting bioinformatics research on rare neurodegenerative disorders. It highlights how multiomics integration can aid in identifying disease-associated genes, molecular pathways, and potential biomarkers, while also addressing current challenges and future opportunities for precision medicine.