In its latest directive, the agency warned that all traders operating in these sections must vacate immediately or risk facing enforcement action.
Officials said the move is part of ongoing efforts to protect road infrastructure and ensure smooth traffic flow along the highway.
The Thika Superhighway is one of the busiest transport corridors in the country, linking Nairobi to several towns in central and eastern Kenya.
Due to its heavy traffic, authorities have repeatedly warned against the illegal occupation of road reserves.
KeNHA noted that over time, a number of traders have gradually set up kiosks, food stalls and small businesses along the highway, especially near busy bus stops and footbridges.
While these businesses serve commuters and residents, the authority insists that operating inside the road reserve creates serious safety concerns.
The agency explained that road reserves are meant to remain clear to allow for future road expansion, maintenance work, and emergency operations.
When the space is occupied by traders or permanent structures, it becomes difficult for engineers to carry out repairs or upgrade projects when needed.
Officials also pointed out that some traders place their goods very close to the highway, forcing customers and pedestrians to stand dangerously near fast-moving vehicles.
This situation increases the risk of accidents, especially during peak hours when traffic is heavy.
KeNHA said the latest notice is not the first warning issued to the traders. The authority explained that previous notices had already been given in an effort to encourage voluntary compliance.
However, many traders reportedly continued with their activities within the restricted area.
The agency has now urged all affected traders to relocate their businesses to legally designated trading spaces provided by local authorities.
It emphasized that enforcement teams may soon begin removing structures that remain within the road reserve after the notice period expires.