Pain Split adds the current HP of the user and target Pokémon. It then divides this value by two and sets the HP of both Pokémon to the result. If the new value is higher than the maximum HP of either Pokémon, that Pokémon will have its HP set to that maximum.
Pain split averages the Pokemon's HP. So yes it would end up with equal HP. This is why Pain-split is good on Pokemon with High Defenses and low HP.