Bernard Bulbwa put Nigeria ahead in the 17th minute when he collected a pass from Musa Yahaya before beating a Botswana defender and shooting the ball into the net, for the only goal of the first-half.
In the second half, the Golden Eaglets overwhelmed Botswana with Ifeanyi Matthew scoring a hat trick in the 53rd, 65th and 69th minutes of the game.
Bulbwa got his second goal of the game in the 57th minute and Musa Yahaya bagged a brace in the 60th and 71st minutes.
After the game coach Garba Manu told newsmen that the team will not rest on their laurels as they are still a work in progress.
The Golden Eaglets are unbeaten in their last 23 competitive and friendly games, during which they have scored 104 goals.