In the 1960s, while working at IBM, Conway invented generalized dynamic instruction handling, a key advancement used in out-of-order execution, used by most modern computer processors to improve performance.

[6] After working as an electronics technician for several years, Conway resumed education at Columbia University's School of Engineering and Applied Science, earning B.S.

[6][7] Conway was recruited by IBM Research in Yorktown Heights, New York, in 1964, and was soon selected to join the architecture team designing an advanced supercomputer, working alongside John Cocke, Brian Randell, Herbert Schorr, Ed Sussenguth, Fran Allen and other IBM researchers on the Advanced Computing Systems (ACS) project, inventing multiple-issue out-of-order dynamic instruction scheduling while working there.

[13] After learning about Harry Benjamin's pioneering research in healthcare for transsexual women, which included the feasibility of sex reassignment surgery, Conway sought his assistance.

Struggling with severe clinical depression due to gender dysphoria, she contacted Dr. Benjamin, who agreed to provide counseling and prescribed hormone replacement therapy, which Conway resumed in 1967.

[23][26] In 1978, Conway served as a visiting associate professor of electrical engineering and computer science at MIT, teaching a now-famous VLSI design course based on a Mead–Conway text draft.

[32][33] VLSI researcher Charles Seitz commented that "MOSIS represented the first period since the pioneering work of Eckert and Mauchley on the ENIAC in the late 1940s that universities and small companies had access to state-of-the-art digital technology.

"[30] The impact and research methods underlying the development of the Mead–Conway VLSI design methodology and the MOSIS prototype are detailed in a 1981 Xerox report,[34] the Euromicro Journal,[35] and several historical overviews of computing.

[43][44] In 1983, Conway left Xerox to join DARPA, where she was a key architect of the United States Department of Defense's Strategic Computing Initiative.

[17] In 2020, National Academy of Engineering President John L. Anderson stated that "Lynn Conway is not only a revolutionary pioneer in the design of VLSI systems ...

But just as important, Lynn has been very brave in telling her own story, and her perseverance has been a reminder to society that it should not be blind to the innovations of women, people of color, or others who don't fit long outdated – but unfortunately, persistent – perceptions of what an engineer looks like.

"[57] In 2023, Lynn Conway collaborated with Jim Boulton to create Lines in the Sand,[58] a short comic book that tells the story of the invention VLSI.

[78][79] Conway and McCloskey accused Bailey of conducting research on human subjects without their knowledge, sending letters to Northwestern University about this alleged misconduct.

Conway alleged Bailey lacked a clinical psychologist license when he wrote letters in support of a young trans woman seeking to transition.

[80] Conway responded, accusing Dreger of misrepresenting the controversy by portraying it as a personal attack on Bailey rather than addressing the broader protest from the trans community.

[81] Conway was a cast member in the first all-transgender performance of The Vagina Monologues in Los Angeles in 2004,[82] and appeared in a Logo documentary film about that event entitled Beautiful Daughters.

[84][85] In 2013, with support from many tech industry leaders, Conway and Leandra Vicci of the University of North Carolina at Chapel Hill lobbied the directors of the Institute of Electrical and Electronics Engineers for transgender inclusion in the their code of ethics.

[14] In 1987, Conway met her husband Charles "Charlie" Rogers, a professional engineer who shared her interest in the outdoors, including whitewater canoeing and motocross racing.