I do not know if this was covered in Brotherhood, but in the manga the name Van Hohenheim was given to slave 23 by
the homunculus Dwarf in the Flask (that later become known as Father) when they first met. Also, the naming didn't have any grand significance. The Dwarf in the Flask just didn't want to keep calling him by a number, so it gifted him a name as thanks for being part of his birth. (His blood was used to bring it to life.)
This happened in episode 40, or chapter 74 in the manga.
Fun fact, Hohenheim was first going to be called Theophrastus Bombastus Van Hohenheim, but the name was too long for him to remember, so a shorter version was chosen.
As I understand it (and as confirmed by the comments), Brotherhood did not change or omit this part compared to the manga.