The striker, who now plays for Liverpool, was awarded for his 2017 performances with Liverpool as well as the Egyptian national team, which has qualified for the 2018 World Cup.
The 25 year old Salah beat his Liverpool team-mate and Senegal winger, Sadio Mane, to the coveted award.
The Egyptian had a sublime year as he led the national side to the African Cup of Nations but failed to win the competition in the final match against Cameroon.
Salah who joined Liverpool from As Roma at the start of the season has scored 17 Premier League goals this term.
In other award categories, Hector Cuper who guided Egypt to qualify for the 2018 World Cup was named the coach of the year whilst Nigerian Assisat Oshoala emerged as the female player of the year. "I want to dedicate this award to all the kids in Africa and Egypt and tell them never stop dreaming and never stop believing", he added.
It is the first time since 1986 that stars from the north of the continent, which along with the west is the strongest football region, have won successive titles.More news: Spurs can not force Harry Kane to stay, admits Pochettino
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Mohamed Salah topped off an incredible 2017 by being crowned the African Player of the Year on Thursday evening. He netted the stoppage time penalty against Congo, which sent the Egyptian team to the world cup competition.
Aubameyang was Bundesliga top scorer with 31 goals last season, holding off Bayern Munich and Poland ace Robert Lewandowski.
Zambian youth player Parson Dhaka was named the youth player of the year, whilst Moroccan team Wydad Athletic Club was the 2017 club of the year.
Salah scored both goals, including the injury-time victor, in the 2-1 win over Republic of Congo in October that sealed Egypt's place at the World Cup. The award is also aimed at improving the development of soccer in Africa.
We hope one day the best player will be based in Africa.