Conway began her career at IBM Research, where she quickly distinguished herself as a talented and innovative computer architect.

Conway made groundbreaking contributions to the design and implementation of dynamic instruction scheduling, a technique that significantly improved the performance of computer processors. Her work during this period was highly influential and laid the groundwork for modern out-of-order execution architectures. She was instrumental in the design of the Advanced Computing System (ACS) project, a highly ambitious supercomputer project.

Due to the societal pressures and lack of understanding surrounding gender identity at the time, Conway was forced to leave IBM after disclosing her intention to transition. This event marked a significant disruption in her career.