Background: Surgical resection is the main treatment for early stage lung cancer; the benefits of surgery, however, need to be weighed against possible complications and patients' quality of life. Methods: We performed a cohort study following patients after video assisted thoracoscopic lobectomy at our tertiary care center. Before surgery, health related quality of life was assessed using the SF-36, the QLQ30, QLQ13 and EQ5D questionnaires. Post-operatively health related quality of life was assessed at regular intervals (2, 4, 8 and 12 weeks). A research team assessed post-operative complications on a daily basis during the patients' hospital stay. Based on the Clavien classification system, the cohort was classified as experiencing high-grade (i.e., grade III or IV) complications or not. Changes in quality of life scores over the follow-up period were compared using linear regression with generalized estimating equations. Results: Between March and September 2011, 44 eligible patients were recruited into the study. The mean age was 65 (SD 8.7) years; 55% were male. The majority (n = 31; 71%) had no or low-grade complications. Patients experiencing high-grade complications reported significantly worse outcomes in the following domains of the SF-36: Global Health, Vitality, and Physical Functioning (p < 0.05 for all). On the QLQ 30 and QLQ 13, patients with high-grade complications had worse outcomes in the dyspnea, emotional function and cognitive function scales, as well as worse shoulder and chest pain, and financial difficulties (p < 0.05 for all). Conclusions: The severity of post-operative complications after video assisted thoracoscopic lobectomy negatively impacts patient centered outcomes postoperatively.