In recent years, research has highlighted the significant role of the immune system in the pathophysiology of catatonia. Emerging evidence indicates that autoimmune encephalitis, such as anti-N-methyl-D-aspartate (anti-NMDA), anti-gamma-aminobutyric acid-A receptor (anti-GABA-AR), and anti-dopamine-2 receptor (anti-D2 R) encephalitis, plays a crucial role in the development of different movement disorders in general and catatonia in particular. In this chapter, we will present three of the most prominent forms of autoimmune encephalitis associated with catatonia depending on their frequency – anti-NMDA, anti-GABA-AR, and anti-D2 R encephalitis. These three neurotransmitter systems, glutamate, GABA, and dopamine, are essential for understanding the pathophysiology of catatonia. Given the rapidly evolving nature of research on autoimmune encephalitis, we aim to inform and sensitize clinicians about the potential association between catatonia (and its signs) and autoimmune encephalitides targeting pathophysiologically relevant neurotransmitters. Our goal is to equip clinicians with the latest findings to improve the recognition and treatment of catatonia in the context of these autoimmune conditions. Finally, we will present the most common red flags that can help identify encephalitis and catatonia early, while emphasizing the need for continued research to better understand the molecular mechanisms and improve treatment options for this complex condition.