Plain English Meaning
A point on your route that you must fly straight over the top of before you start turning toward the next point.
Full Definition
A waypoint that requires the aircraft to pass directly over the point before initiating any turn to the next leg of the route. The turn is not anticipated; it begins only after the waypoint has been crossed.
Context Anchor
Seen on GPS/RNAV routes, instrument procedures, and navigation charts when the route requires the aircraft to pass over a specific point before changing direction.
Derivation
“Waypoint” means a point along the way of travel. “Fly-over” is used in its direct aviation sense: the aircraft is expected to pass over that point, not just near it or around it.