Aircraft accidents over the last decade have raised questions about the most effective way to transition pilots onto new aircraft automation systems. This debate can range from the details contained within aircraft flight manuals to computer-based versus simulator-based training. While some questions are still under consideration, most fall short in the understanding of how pilots “actually” learn. The researchers conducted a longitudinal study focusing on pilot learning; through interviews, observations, and field documentation, 10 pilot trainees from two regional airlines were followed for 5 months throughout their initial airline training. Using joint cognitive systems theory, and concepts from curriculum theory to understand the utility of training programs, the study revealed gaps between the airlines’ intended learning outcomes and the trainees’ actual experiences. The findings demonstrate that automation, as opposed to other aircraft systems, may require different approaches to learning. Recommendations for possible modifications to current pilot training are discussed.