[7] Eritrea participated in the 1994 CECAFA Cup, organised by the Council for East and Central Africa Football Association,[7] even though the ENFF was not founded until 1996.

They finished second in their three team group, and advanced to a playoff round where they faced Senegal and Zimbabwe, but ultimately lost all four matches in that final stage.

[20] On 2 March 2022, Eritrea withdrew from the preliminary round of the 2023 Africa Cup of Nations qualifiers due to the lack of a stadium that meets the requirements set by CAF to host its international matches.

In November 2023, Eritrea, who were drawn into Group E alongside Morocco, Zambia, Tanzania, Congo and Niger,[23] pulled out of the 2026 World Cup qualifiers, citing the reason as being the refusal of Zemede Tekle, who is the Eritrean Commissioner for Sports and Culture, to participate in the playoffs.

[17][24][25] Recent years have seen a high number of refugees leaving Eritrea,[26][27] and some athletes travelling to competitions abroad have taken the opportunity to abscond.

[28] In December 2012, 17 Eritrean footballers and the team's doctor vanished after the CECAFA championship tournament in Uganda and all applied for asylum in the country.

[29][30][31] Four players of Red Sea FC defected after a CAF Champions League 2006 match in Nairobi, Kenya,[32] and up to 12 members of the national side after the 2007 CECAFA Cup in Tanzania.

[38] Given the number of players seeking asylum, the Eritrean government began requiring athletes to pay a 100,000 nakfa surety before traveling abroad.

[42] Nicholas Musonye, the secretary-general of CECAFA, feared that the government might react by refusing to let the team travel abroad in future.

[43] Eleven of these players have since travelled to Adelaide in Australia[44] with two of them, Samuel Ghebrehiwet and Ambes Sium, signing for Gold Coast United in the A-League in August 2011.

[47] A few months later in December, a further seven players selected for the international team refused to return home and sought asylum in Uganda after a tournament.