Lookman succeeds compatriot Victor Osimhen, who last year became the first Nigerian winner since Nwankwo Kanu in 1999.
The 27-year-old owes his achievement to consistently excellent performances both for Nigeria and current Serie A leaders Atalanta.
His three goals helped Nigeria reach the 2024 Africa Cup of Nations final, where they led hosts the Ivory Coast before losing 2-1 in Abidjan.
Lookman struck both goals in a last-16 victory over Cameroon and the winner in a 1-0 quarter-finals win over Angola.
A few months after the AFCON, the London-born attacker scored a hat-trick as Atalanta overcame Bayer Leverkusen 3-0 in the Europa League final in Dublin.
"This is something incredible. To the youth of Africa I say -- never give up. Turn pain to power," Lookman said after receiving the award.
The runners-up included South African Ronwen Williams, who won the best goalkeeper and best club player awards.
Instead of the traditional three nominees for the best player award, there were five given the closeness of the voting among the coaches and captains of African national teams.
The other runners-up were Morocco full-back Achraf Hakimi, Ivory Coast winger Simon Adingra and Guinea forward Serhou Guirassy.
Banda best woman
Zambia forward Banda won the women's player of the year award in recognition of her many goals for American club Orlando Pride and her country.
Banda scored four goals for Zambia at the 2024 Paris Olympics, including a hat-trick in a group-stage loss to Australia.
Her 13 regular season goals and four in play-offs helped Orlando Pride win the National Women's Soccer League for the first time.
The runners-up were Morocco forward Sanaa Mssoudy and Nigeria goalkeeper Chiamaka Nnadozie, who were both winners in other categories.
Award winners
Men
Player of the Year
Ademola Lookman (NGR)
Club Player of the Year
Ronwen Williams (Mamelodi Sundowns/RSA)
Goalkeeper of the Year
Ronwen Williams (RSA)
Young Player of the Year
Lamine Camara (SEN)
Coach of the Year
Emerse Fae (CIV)
National Team of the Year
Ivory Coast
Club of the Year
Al Ahly (EGY)
Best X1
Andre Onana (CMR); Achraf Hakimi (MAR), Kalidou Koulibaly (SEN), Chancel Mbemba (COD); Mohammed Kudus (GHA), Sofyan Amrabat (MAR), Franck Kessie (CIV), Yves Bissouma (MLI); Mohamed Salah (EGY), Victor Osimhen, Ademola Lookman (both NGR)
Women
Player of the Year
Barbra Banda (ZAM)
Club Player of the Year
Sanaa Mssoudy (FAR Rabat/MAR)
Goalkeeper of the Year
Chiamaka Nnadozie (NGR)
Young Player of the Year
Doha El Madani (MAR)
Coach of the Year
Lamia Boumehdi (TP Mazembe/COD)
National Team of the Year
Nigeria
Club of the Year
TP Mazembe
Best XI
Andile Dlamini (RSA); Michelle Alozie, Osinachi Ohale (both NGR), Lebohang Ramalepe, Karabo Dlamini; Linda Motlhalo (all RSA), Rasheedat Ajibade (NGR), Ghizlane Chebbak (MAR); Barbra Banda (ZAM), Asisat Oshoala (NGR), Tabitha Chawinga (MAW)
