Daniel Caron resigned after billing taxpayers nearly $4,500 for personal Spanish lessons.
Heritage Minister James Moore, who's responsible for the institution, had called Caron's actions out of line and met with him this month after the revelations came to light.
"Minister Moore thanks Mr. Caron for his service and wishes him well in all his future endeavours," said a statement from Moore's office.
A spokesman for Library and Archives confirmed Caron's departure but provided no details. Caron notified staff of his departure in an email late Wednesday afternoon.
The issue arose after the QMI news agency reported Caron spent $4,482 in 2011-12 to learn Spanish.
He also signed up for another $10,000 worth of lessons, which were contracted for the following two years, but Library and Archives said no further money was spent.
The library said the lessons were in compliance with contracting guidelines. A spokesperson said at the time that Caron took the classes to have a basic ability in Spanish for international conferences.
The scandal over his expenses followed controversy over a new code of conduct for employees at the library.
The code deemed activities such as teaching, speaking at conferences and other personal engagements as "high risk" and required them to be cleared in advance with managers, even if they were done on personal time.
Caron was appointed head librarian and archivist of Canada in 2009, taking over the institution as it struggled to transform its collections for the digital world with reduced budgets.
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