Fungal metabolites have received so much attention due to the immense potential of these fungal natural products in health, agriculture and the environment. Now, like other metabolites in other organisms, fungal metabolites can also serve as indicators of the shifts in the biological and physiological states of fungal cell, and this has fuelled the rise of metabolomics. Metabolomics is a rapidly advancing field dedicated to the comprehensive analysis of the entire metabolome of an organism and combines biology, microbiology, chemistry and bioinformatics to provide a holistic understanding of the biochemical processes of an organism. This chapter listed analytical tools used in metabolomics and the application of metabolomics to fungal research. Key analytical techniques used to detect, characterize and isolate metabolites, such as nuclear magnetic resonance (NMR) and mass spectrometry (MS), will be emphasized. Also, the combination of metabolomics with other technologies in the field of omics including genomics, transcriptomics and proteomics will be presented. Web-based and software-based data analysis tools used in metabolomics research will also be discussed. The chapter concludes with the current trends in fungal metabolomics studies to know the fundamental role this research will have in future.