When does Son Goku learn to fly? In chapter 202 of the DragonBall manga, Goku floats into the air to see where his child is:



Then when he is travelling along the green scale road, he flies a portion of the way there. He also flies to assist combatting the Saiyans after his training with the Lord of the Worlds.

When did Goku learn how to fly, when previously he had only used Kintou for aerial movement?
It was never shown, how he learned to fly, so that's pure speculation. The DragonBall-Wiki has a possible explanation:


  Goku likely learned how to fly from Kami during his long training at Kami's Lookout, as he was unable to do so before and demonstrated his abilities to conclude his World Martial Arts Tournament fight with Piccolo.


Source: Dragonball Wiki