In the quest to identify novel biomarkers for pulmonary tuberculosis (TB), high-throughput systems biology approaches such as metabolomics has become increasingly widespread. Such biomarkers have not only successfully been used for better disease characterization, but have also provided new insights toward the future development of improved diagnostic and therapeutic approaches. In this review, we give a summary of the metabolomics studies done to date, with a specific focus on those investigating various aspects of pulmonary TB, and the infectious agent responsible, Mycobacterium tuberculosis. These studies, done on a variety of sample matrices, including bacteriological culture, sputum, blood, urine, tissue, and breath, are discussed in terms of their intended research outcomes or future clinical applications. Additionally, a summary of the research model, sample cohort, analytical apparatus and statistical methods used for biomarker identification in each of these studies, is provided.