Background: The proximity of craniopharyngiomas (CPs) to critical neurovascular structures can lead to a host of neurologic and endocrine complications that lead to difficulty with surgical management. In this review, we examine the molecular and genetic markers implicated in CP, their involvement in tumorigenic pathways, and their impact on CP prognosis and treatment. Methods: We undertook a focused review of relevant articles, clinical trials, and molecular summaries regarding CP. Results: Genetic and immunological markers show variable expression in different types of CP. BRAF is implicated in tumorigenesis in papillary CP (pCP), whereas CTNNB1 and EGFR are often overexpressed in adamantinomatous CP (aCP) and VEGF is overexpressed in aCP and recurrent CP. Targeted treatment modalities inhibiting these pathways can shrink or halt progression of CP. In addition, EGFR inhibitors may sensitize tumors to radiation therapy. These drugs show promise in medical management and neoadjuvant therapy for CP. Immunotherapy, including anti-interleukin-6 (IL-6) drugs and interferon treatment, are also effective in managing tumor growth. Ongoing clinical trials in CP are limited but are testing BRAF/MET inhibitors and IL-6 monoclonal antibodies. Conclusions: Genetic and immunological markers show variable expression in different subtypes of CP. Several current molecular treatments have shown some success in the management of this disease. Additional clinical trials and targeted therapies will be important to improve CP patient outcomes.