She starts her new roles with immediate effect, with Richard Gould now installed as chief executive on a full-time basis after leaving his most recent post with Bristol City Football Club at the end of January.
The ECB said in a press release that Connor would work closely with Gould on "board-level leadership responsibilities" and that her initial focus would be managing the "game-wide response" to the Independent Commission for Equity in Cricket's upcoming report into diversity and inclusion within the sport.
Connor said: "It was an enormous honour to have served as interim CEO of ECB, and I'm delighted that in this new role I can continue to make a difference across the game as we strive to become a more inclusive sport. Cricket's response to the Independent Commission for Equity in Cricket's report will be a vital moment for our game and we must use it to change for the better.
"Throughout my many years working in cricket so far, I have been committed to making our game one which includes and welcomes people from every background, and that's what will continue to drive me on in everything I do."
Gould said: "This is a huge year for cricket, with the men's and women's Ashes to look forward to, the women's game developing so quickly and domestic cricket on a fast growth strategy, while we also have the challenges of the Independent Commission for Equity in Cricket report to come.
"I am delighted therefore that Clare has accepted the role of Deputy CEO and MD England Women. She did an excellent job as Interim CEO, and prior to this as MD Women's Cricket. The new role will allow her to continue to lead and influence across the game, allowing us all to benefit from her experience and knowledge."
Connor's previous role as managing director of women's cricket will not be replaced. Beth Barrett-Wild, who oversees the women's Hundred, will instead have her remit expanded, becoming director of the women's professional game.