Lynn Conway was born as a biological male in Mount Vernon, New York. Early in life, she experienced a strong sense of gender incongruence, a feeling that significantly shaped her personal experiences and later fueled her advocacy work. These feelings were kept secret and suppressed due to the societal norms of the time.

Conway earned a Bachelor of Science in Physics and a Master of Science in Electrical Engineering from Columbia University. She began her career at IBM in the 1960s, where she made significant contributions to computer architecture. Most notably, she is credited with crucial innovations in dynamic instruction scheduling, a core component of modern computer processors.