The 28-year-old scored 17 goals in 24 games last term to help Malanti Chiefs finish sixth in the topflight standings.
Molapo, who was born in Balfour, previously trained with University of Pretoria but no deal was forthcoming at the time.
"There's a boy that is coming from Swaziland, Charles Molapo, who was top goal scorer and playing for Malanti Chiefs.
"He has signed now with Baroka FC," says former Kaizer Chiefs defender Abel Shongwe, who represents Molapo.
Bakgaga also recently added Elvis Chipezeze, Tshediso Patjie, Bheki Maliba, Bonginkosi Makume, Siseko Manana, Armand Gnanuillet, Ananias Gebhardt, Shabani Hussein and Orebotse Mongae to their roster.
Meanwhile, the arrival of new coach Wedson Nyirenda has precipitated the exit of technical director Doctor Khumalo.