Anti-glomerular basement membrane (anti-GBM) disease is an extremely rare small vessel vasculitis, which typically presents as rapidly progressive glomerulonephritis with or without pulmonary hemorrhage. Atypical anti-GBM disease varies in its clinical and laboratory presentation with insidious onset of symptoms. We present the case of a 16-year-old male child who presented with a two-week history of fever, weight loss, cough, hemoptysis, shortness of breath, and a five-year history of intermittent emesis. A computerized tomography of the chest demonstrated diffuse miliary pulmonary nodules with a "tree-in-bud" pattern. Serologic evaluation was negative for anti-nuclear, double-stranded, and anti-neutrophilic cytoplasmic antibodies. Urinalysis was negative for hematuria and proteinuria, but anti-GBM antibodies were elevated. Kidney biopsy demonstrated linear immunofluorescence staining of glomerular basement membrane with immunoglobulin G (IgG) without active crescent formation or necrosis. Lung biopsy demonstrated occasional hemosiderin-laden macrophages, patchy peribronchial and interstitial lymphocytic inflammation, interstitial and alveolar septal fibrosis, and emphysema. The patient was diagnosed with atypical anti-GBM disease based on the circulating and tissue-bound antibodies on kidney and lung biopsy and chronic alveolar bleeding, and improved with treatment with intravenous steroids, cyclophosphamide, and rituximab. This case report highlights the importance of a high index of suspicion for this disease and the need to perform a renal biopsy even in the absence of hematuria or proteinuria. Additionally, this case was unusual as the patient presented primarily with pulmonary and gastrointestinal symptoms and normal renal functions. His pathology was limited to linear immunofluorescence without active crescent formation, and this has not been previously reported, to our knowledge.