The deceased, identified as Lamdah Anjah who worked as a mechanic, was believed to be heading towards Jalan Tuaran By-pass from Jalan Gudon when the tragedy occurred about 11.50pm.
The impact caused the motorcyclist to sustain severe head injuries.
The van driver who escaped unscathed was said to be heading towards Taman Cerah from Kota Kinabalu.
Traffic police Sergeant Jenuil and Sergeant Abang were at the scene.
In another accident, another motorcyclist sustained serious injuries when his motorcycle collided with a Honda vehicle near Sadong Jaya, here, Saturday.
The motorcyclist, in his 20s, was believed to be heading towards the Wawasan Plaza direction from Karamunsing when the mishap occurred about 4.45pm.
The 42-year-old Honda driver, who escaped unscathed, was said to be heading towards Sadong Jaya from Centre Point.
The motorcyclist was subsequently sent to the hospital by a pickup driver plying the route.
Traffic police Sergeant Wasli was at the scene.