How do you get the second master ball on ruby?

You can't get a second Master Ball in Ruby. You only receive one Master Ball in the game, and it's given to you by Professor Birch at the start.

While there are many rumors about hidden Master Balls or ways to get more, these are all false.

Remember: The Master Ball is a very powerful item, designed for catching extremely difficult Pokemon. It's best to save it for those truly challenging catches!