Current methods for Gamma Knife (GK) treatment planning utilizes either manual forward planning, where planners manually place shots in a tumor to achieve a desired dose distribution, or inverse planning, whereby the dose delivered to a tumor is optimized for multiple objectives based on established metrics. For other treatment modalities like IMRT and VMAT, there has been a recent push to develop knowledge-based planning (KBP) pipelines to address the limitations presented by forward and inverse planning. However, no complete KBP pipeline has been created forGK. To develop a novel (KBP) pipeline, using inverse optimization (IO) with 3D dose predictions for GK. Data were obtained for 349 patients from Sunnybrook Health Sciences Centre. A 3D dose prediction model was trained using 322 patients, based on a previously published deep learning methodology, and dose predictions were generated for the remaining 27 out-of-sample patients. A generalized IO model was developed to learn objective function weights from dose predictions. These weights were then used in an inverse planning model to generate deliverable treatment plans. A dose mimicking (DM) model was also implemented for comparison. The quality of the resulting plans was compared to their clinical counterparts using standard GK quality metrics. The performance of the models was also characterized with respect to the dosepredictions. Across all quality metrics, plans generated using the IO pipeline performed at least as well as or better than the respective clinical plans. The average conformity and gradient indices of IO plans was 0.737 0.158 and 3.356 1.030 respectively, compared to 0.713 0.124 and 3.452 1.123 for the clinical plans. IO plans also performed better than DM plans for five of the six quality metrics. Plans generated using IO also have average treatment times comparable to that of clinical plans. With regards to the dose predictions, predictions with higher conformity tend to result in higher quality KBP plans. Plans resulting from an IO KBP pipeline are, on average, of equal or superior quality compared to those obtained through manual planning. The results demonstrate the potential for the use of KBP to generate GK treatment with minimal humanintervention.