Non-Hodgkin lymphoma (NHL) includes a diverse group of hematological malignancies. The common site for extranodal involvement of NHL is the gastrointestinal tract (GIT), with the stomach being the most prevalent site. The appendix is a very unusual site of involvement in NHL. This case report describes an uncommon instance of an appendicular mass in an elderly female who complained of vomiting for two weeks, as well as abdominal pain, and was radiologically suspected to have appendicular malignancy. A right hemicolectomy was done, and she was diagnosed with extranodal mucosa-associated lymphoid tissue (MALT) lymphoma involving the appendix. Postoperatively, she also developed thrombo-occlusive disease in her right lower limb, with right foot dry gangrene, for which thromboembolectomy was done. Later, a below-knee amputation was carried out. Lymphoma associated with thrombophilia is a rare presentation and not many cases have been reported in the literature. We present this case here on account of the rarity of lymphoma involving the appendix with associated thrombophilia.