Bolton, currently the RFL's director of projects and planning, will take up her new role next month.
She will become managing director of the organising committee for the the IAAF World Championships and the International Paralympic World Championships, which are being staged in the same city for the first time.
Bolton, a former chief executive at Wigan, said: "I will leave rugby league with nothing but fond memories and pride at having had the opportunity to work with, and alongside some very talented and passionate people.
"To be able to help deliver Rugby League World Cup 2013 was a real privilege, not least because the tournament allowed us to present the sport in all its glory."
UK Athletics c hief executive Niels de Vos said: "We are delighted to have recruited a leader of Sally's calibre. She was the outstanding candidate for a role which attracted global interest.
"She has precisely the hands-on delivery experience we are after, and has the accolades to prove it from her successful leadership of the 2013 Rugby League World Cup."
RFL chief executive Nigel Wood said: "On behalf of the whole sport I would like to place on record our sincere thanks to Sally for her important contribution over the last seven years.
"The excellence of our events, including RLWC2013, has reinforced rugby league's standing as a world-class sport and Sally has been a key figure in that."
- Sports & Recreation
- Board & Management Changes