Brothers Union (2002–present) Following his retirement, Amer was named the executive director and team manager of
Brothers Union in 2002. He found early success as Brothers lifted their first Dhaka Premier Division League title in the 2003–04 season without a full-time head coach, as both
Syed Nayeemuddin and S M Abu Noman Nannu served as coaches during games. Amer was eventually made the general secretary of
Little Friends Club, which serves as the junior team to Brothers. On 5 August 2012, Amer Khan declared on
Ekattor TV that Brothers Union were forced to play a fixed match against eventual champions,
Abahani Limited Dhaka, on 26 May of the same year in the
2012 Bangladesh Premier league. Amer stated
"Is it too difficult to understand how we lost 2-4 against Abahani when they were playing with 10 men? We had to do so because there were specific instructions given to us to lose. When an influential political leader tells you to throw away the match, what else could you do?" On 9 August 2012, Amer claimed that his comments regarding the fixed match were aired out of context. Eventually, the vice president of the
Bangladesh Football Federation (BFF) at the time,
Abdus Salam Murshedy, later revealed that the league committee would handle the matter instead of the Fixed-Match Identification Committee. Following Brothers' relegation from the Premier League in the
2020–21 season, Amer informed that the club would not participate in the
2021–22 Championship League (second-tier) due to financial difficulties while also criticizing the BFF's decision to relegate the club during the
COVID-19 pandemic. Nevertheless, the club returned to the top-flight by winning the Championship League the
following season.
Bangladesh Football Federation (2020–present) Amer served as the team manager of the
Bangladesh U19 national team in both 2014 and 2019. However, he tested positive for COVID-19 when the team traveled to Doha, Qatar for the
2022 FIFA World Cup qualification – AFC second round. In June 2023, Amer was reappointed as the team manager of the Bangladesh national team for the
2023 SAFF Championship. ==Personal life==