Background The purpose is to delineate the clinical and pathological characteristics of rare primary malignant pulmonary tumors in children. Methods Utilizing the National Cancer Data Base (NCDB), we analyzed all children (≤ 18 years) with a primary malignant pulmonary tumor from 1998 to 2011 to identify factors associated with better survival. Results Of 211 children identified, the most common histology was carcinoid tumor (n = 133, 63%) followed by mucoepidermoid carcinoma (MEC) (n = 37, 18%), squamous cell carcinoma (SCC) (n = 19, 9%), adenocarcinoma (n = 16, 8%), bronchoalveolar carcinoma (BAC) (n = 4, 2%), and small cell carcinoma (SCLC) (n = 2, < 1%). Factors that significantly affected survival include histology, race, tumor size, lymph node status, and extent of surgery. Patients with MEC and carcinoid tumors had a better overall survival compared to patients with other histologies (p < 0.0001). The 5-year overall survival for MEC and carcinoid tumors was 100% and 95% (95% CI 87-98), respectively, versus 50% (95%CI 1-91) for BAC, 28% (95%CI 9-52) for SCC, and 26% (95%CI 5-55) for adenocarcinoma. Conclusion The majority of pediatric patients with a primary malignant pulmonary tumor present with carcinoid tumor or MEC and have an excellent prognosis. Lung cancers which are common in adults, but rare in children, have a worse prognosis.