In his letter, O'Brien calls it "an honour and privilege" to have worked with everyone at the Senate — especially, he notes, senators — throughout his tenure in the Red Chamber.
"You have accomplished great things and I am so proud to have been part of it," O'Brien says.
He also pledges to maintain his support for the embattled Upper House.
'Will continue to advocate' on behalf of Senate
"I am a firm believer in bicameralism, in the policy and legislative contributions that the Senate makes, and I sincerely believe that our committee system is second to none," he notes.
"I will continue to advocate on behalf of the Senate in my retirement."
O'Brien, who was appointed to his current post in 2009, has a parliamentary resume that extends back for nearly four decades, including stints working in the Library of Parliament and the House of Commons before moving to the Senate in 1980.
As clerk, he acts as both senior procedural adviser to the Senate speaker and head of Senate administration.
According to his letter. O'Brien will stay on until Feb. 13, 2015.
Auditor general to release findings next spring
That will see him leave just weeks before Auditor General Michael Ferguson is expected to hand down his report on Senate expenses.
In his role as administrative chief, O'Brien worked closely with the Senate internal economy committee during its preliminary investigations into expense claims filed by Senators Patrick Brazeau, Mike Duffy, Mac Harb and Pamela Wallin.
Brazeau, Duffy and Wallin are currently suspended from the chamber, while Harb resigned his seat on Aug. 26, 2013.