Champions Super Falcons were given a first round bye alongside Equatorial Guinea, South Africa and Cameroon.
Falcons opponent Gambia lost 2-1 to Burkina Faso in their first leg encounter at the 4 Août Stadium, Ouagadougou on 7th of April. A 2-1 win by the Gambians in Bakau on Tuesday, forced the game to penalties where they won 5-3 on aggregate.
Gambia and the Super Falcons will face each other in June.
Meanwhile, 2016 AWCON runners-up Cameroon will take on Congo who defeated Central African Republic 3-1 on aggregate in the first round.
The seven winners of the second round will join hosts Ghana in the final tournament scheduled for 17 November to 1 December 2018.
The three top nations in the continental competition will qualify for the 2019 World Cup in France.
AWCON Second round qualifiers fixtures
Algeria vs Ethiopia
Côte d’Ivoire vs Mali
Gambia vs Nigeria
Congo vs Cameroon
Kenya vs Equatorial Guinea
Lesotho vs South Africa
Zambia vs Zimbabwe