Track replacement is taking place in the Newcraighall area over three Sundays - 4, 11 and 18 June.
Journey times on the line will be extended and buses will replace trains between Edinburgh and Gorebridge.
Rail services will run as normal on the rest of the line. Customers have been advised to check train times on the ScotRail app or website.
A ScotRail Alliance spokesperson said: "We appreciate our customers' patience while we undertake these vital works."
Passengers on the Borders Railway have been advised to check their journeys in advance ahead of engineering work.