Myalgic Encephalomyelitis (ME), also known as Chronic Fatigue Syndrome (CFS), is a highly debilitating multisystem illness affecting millions of people worldwide. Patients typically experience overwhelming fatigues, chronic inflammation, cognitive impairment, and post-exertional malaise (PEM), a hallmark symptom marked by exacerbation of symptoms following any physical or mental exertion. While the etiology of this disease remains unclear, mounting evidence points to the immune system being a key contributor to ME/CFS pathophysiology. Nonetheless, our current understanding of ME/CFS leukocytes is limited by the lack of quantitative and temporal resolution required to effectively profile the complex interplay between leukocyte populations. To comprehensively characterize the gene regulatory state and identify the cell types driving immune dysregulation in ME/CFS patients and during PEM, we generated single cell atlases of transcription and chromatin accessibility of peripheral blood mononuclear cells in matched patient and control cohorts at baseline and after symptom provocation. We identified widespread dysregulation in ME/CFS, as classical monocytes expressed markers suggestive of inappropriate differentiation, intercellular communication, and tissue migration; while CD8+ T cells displayed signs of altered metabolism and epigenetic scarring which primes them towards exhaustion. We further observed extensive reprogramming at transcription factor binding sites in these populations, including upregulation of NF-κB family TFs in specific monocyte lineages, and increased activity of exhaustion-associated TFs such as Eomes and T-bet in CD8+ T cells. Taken together, these data dissect the molecular basis of immune dysfunction as a core driver of ME/CFS and provide a basis for future therapies, such as checkpoint blockade, metabolic interventions, or drugs that target chronic viral infections.