Mycoplasma pneumoniae (M. pneumoniae) infections typically affect the respiratory system but can also present with extrapulmonary manifestations, including gastrointestinal involvement. We report the case of a four-year-old boy who presented with abdominal pain and fever, with minimal respiratory symptoms throughout the course of his illness. Despite initial treatment with clarithromycin, his symptoms persisted, and the chest radiographic findings showed worsening pneumonia. Imaging revealed small bowel fluid retention and impaired intestinal motility, suggesting gastrointestinal involvement likely mediated by immune mechanisms. Laboratory findings included elevated lactate dehydrogenase (LDH) levels and mild liver dysfunction, consistent with systemic inflammation. The patient was treated with tosufloxacin and corticosteroids, which led to clinical improvement and symptom resolution. This case highlights the diagnostic challenge posed by atypical presentations of M. pneumoniae infection, particularly in young children with minimal respiratory symptoms. Intestinal involvement, although rare, should be considered a potential extrapulmonary manifestation. Elevated LDH levels and poor response to macrolide therapy can indicate refractory or macrolide-resistant cases, necessitating alternative treatments such as corticosteroids and fluoroquinolones. Clinicians should be aware of these atypical presentations to ensure early diagnosis and tailored therapy, improving outcomes in pediatric patients with unusual manifestations of M. pneumoniae infections.