The Black Stars finished on two points in Group B, drawing 2-2 with both Egypt and Mozambique following a 2-1 defeat by Cape Verde in their opener.
Ghana had distant hopes of progressing as one of four best-ranked third placed sides, but were eliminated on Tuesday when results went against them.
Hughton had been appointed as Ghana head coach in February last year.
“Chris Hughton has been relieved of his duties with immediate effect,” a Ghana Football Association (GFA) statement said., external
“The executive council has also taken a decision to dissolve the technical team of the Black Stars.
“The GFA will in the coming days provide a roadmap on the future direction of the Black Stars.”
Former Newcastle United and Brighton boss Hughton began working as a technical adviser for the four-time continental champions in February 2022.
He replaced Otto Addo as boss after Addo stepped down following the 2022 World Cup in Qatar, where Ghana finished bottom of Group H with one win from three matches.
Ghana also exited the 2021 Afcon finals in Cameroon at the group stage, and the West Africans suffered the same fate in Ivory Coast.
The GFA said it was “100%” behind Hughton after a fan had a “verbal altercation” with the coach following their shock defeat by Cape Verde.
It had looked like the 65-year-old would guide the Black Stars to the last 16, with Ghana sitting second in Group B while holding a 2-0 lead over Mozambique in their final group game.
However, the Mambas scored twice in second-half stoppage time to clinch an unlikely draw which ultimately sent the Ghanaians home.
The West Africans had also endured a mixed start to 2026 World Cup qualifiers under Hughton, beating Madagascar with a stoppage-time goal before losing 1-0 in Comoros.
