The 1999 season of the Liga de Fútbol Profesional Boliviano was the 42nd season of top-tier football in Bolivia.
San José (Oruro) relegated; Atlético Pompeya and Mariscal Braun promoted
| Pos | Name | Team | Goals | |
|---|---|---|---|---|
| 1 | Víctor Hugo Antelo | Blooming | 31 | |
| 2 | Antonio Vidal González | The Strongest | 30 | |
| 3 | Leonel Liberman | Unión Central | 25 | |
| 4 | Joaquín Botero | Bolívar | 24 | |
| 5 | Limberg Gutiérrez | Blooming | 23 | |
| 6 | Milton Coimbra | Oriente Petrolero | 20 | |
| 7 | Miguel Angel Mercado | Bolívar | 19 | |
| 8 | Marcelo Ceballos | Guabirá | 15 |