Lymphatic vessel dysplasia is associated with Fontan-associated protein-losing enteropathy. Extra nodal non-Hodgkin lymphomas including mucosa-associated lymphoid tissue (MALT lymphoma) are associated with lymphatic vessel dysplasia. Here, we describe the case of a 7-year-old with Fontan-associated protein-losing enteropathy who developed MALT lymphoma with a clinical course indicative of interaction between these pathologies and improvement in protein-losing enteropathy after MALT lymphoma treatment. This case suggests a pathophysiologic overlap which has implications for the management of Fontan-associated protein-losing enteropathy.