The AFC U-16 Championship took place in Uzbekistan from 4 to 19 October 2008. Iran, Japan, Korea Republic and UAE all booked passage to the finals.

The eighth African U-17 Championship took place in Algeria from 19 March to 3 April 2009. Gambia, Algeria, Malawi and Burkina Faso qualified for the finals in Nigeria.

The final round of the European U-17 Championship 2008/09 took place in Germany from 6 to 18 May 2009. Germany, the Netherlands, Italy, Switzerland, Spain and Turkey booked their places by finishing in the top three of their respective groups.

The qualifying tournament for North, Central America and the Caribbean zone took place in Tijuana, Mexico in late April. The United States and hosts Mexico both won their groups and will be joined in Nigeria by runners-up Honduras and Costa Rica. The competition was halted after the group stages due to an outbreak of swine flu in Mexico.

The OFC U-17 Championship took place in Auckland, New Zealand between 20 and 24 April 2009. The host nation won the competition to qualify for the FIFA U-17 World Cup Nigeria 2009.

Argentina became the first team to qualify from the tournament in Iquique, Chile, which ran from 17 April to 9 May 2009, but it was Brazil who emerged as continental champions, beating Argentina in the final on penalties. Colombia and Uruguay earned the remaining spots for the FIFA U-17 World Cup Nigeria 2009.

The host country qualifies automatically.