Ms Logan, who was given extra powers to run the council during lockdown, has been in the £120,000 post for nine years, and was previously the council’s director of resources.
She has worked at SBC since 2006, when she became head of human resources.
Council convener David Parker said: “Tracey has been an innovative, effective and highly-regarded chief executive who has been at the forefront of modernising the council for nearly 10 years.
“There will be time for me to pay a more fulsome tribute before Tracey leaves us at the end of September, but her work on the Inspire Learning programme, her strong leadership and the way she has put the council on a sustainable financial footing are among the many achievements and strengths worth highlighting.
“She is a highly respected local government officer who is well regarded as a strategic leader and has been at the forefront of many innovative changes in the Borders. I can honestly say that I have not worked with a more talented and effective local government officer.”
Ms Logan said: “Being chief executive has been an enormous privilege and I will miss working with the outstanding and dedicated council staff we have in the Borders.
“The events of the past year, in particular, have presented us with some the biggest challenges in my entire career and indeed the history of the council.
“Since November we have dealt with the Peebles High School fire, which saw us create a temporary school across multiple sites before returning our young people to the original school.
“Severe weather and flooding hit the Borders shortly afterwards, causing widespread damage to local communities.
“There was then a general election and also a very short timescale to deliver our budget.
“This was followed, of course, by the Covid-19 pandemic.
“These challenges have been significant and the staff across all departments and services have been incredible in their response.
“The council will soon confirm details on the recruitment process to appoint a new chief executive.
“However, I still have work to do before I leave at the end of September and as ever will do all I can to lead this council to the best of my ability in these challenging circumstances.”