In July 2000, Lee joined Crystal Palace and spent five years working as a football development officer before sharing his role and working as a coach within the club's youth academy. In 2003, while still working for Crystal Palace, Lee became an FA Learning Tutor for The Football Association and instructed courses for professional football clubs, county football associations, colleges and universities.
In July 2014, Lee signed a two-year contract to become the National Technical Director of Rwanda, making him at the time one of the youngest technical directors in world football. He was responsible for development, management and implementation of the federation's national programmes which include grassroots, coach education, women's and girls' football and elite player development. Since his appointment the federation has introduced youth leagues across the country for both boys and girls. To help support this programme, Lee worked to restructure the coach education programme and developed strong partnerships with The Football Association and the German Football Federation to introduce grassroots and leadership programmes to promote standards and increase the level of coaching across the country. In addition to his role Lee coached the U17s and U23s National teams to compete in the AFCON qualifiers and international friendlies. In January 2015, he was appointed the interim National Team Coach following the resignation of the much admired Stephen Constantine who left to become the National Team Coach of India. In July 2014, national team were ranked 134th in the world and after a run of successful results Rwanda moved up to 64th in the FIFA world rankings, the highest position for the country as of 2015
On 14 April 2015, it was announced that Johnson would be taking charge of the India U19 and would join Stephen Constantine coaching staff as his assistant.
In July 2017, Lee was appointed Head of Coaching at Barnet Football Club.
Coaching Conventions
Lee has worked as a consultant and has delivered coach education programmes, workshops and seminars for a number of professional organisations and associations, one of which was Inside Soccer. In August 2012, Lee was featured as a guest clinician at the Inside Soccer International Coaches Convention which took place in New York. Lee also spent time filming a number of coaching sessions on youth development. Since 2012, Lee has been featured at a number of coaching conventions around the world. In 2014, he delivered a session at the NSCAA Convention "Philly 2014".
