Atypical pneumonia refers to a group of lower respiratory tract infections caused by specific respiratory pathogens that differ clinically and radiologically from typical bacterial community-acquired pneumonia (CAP). These infections involve both zoonotic and non-zoonotic transmission routes, with non-zoonotic cases being more common. A key distinguishing feature of atypical CAP is its frequent extrapulmonary involvement, which distinguishes it from the classic presentation of CAP. Therefore, recognition of clinical syndromes plays an important role in increasing clinical suspicion, guiding the initiation of empirical antibiotic therapy, and supporting targeted diagnostic evaluations. This review aims to consolidate current knowledge to improve the understanding and clinical recognition of atypical pneumonia. We performed a comprehensive literature search on PubMed, focusing on the clinical presentation, diagnostic approach, and management of atypical pneumonia. The causative pathogens are often associated with systemic effects and a wide range of extrapulmonary manifestations. Furthermore, some of these organisms pose challenges in laboratory identification due to their difficulty in cultivation and the risks associated with isolation. Consequently, syndromic diagnosis remains essential in initiating timely treatment and directing further diagnostic workup.