The move will allow the incumbent, Sir Malcom McKibben, to focus on his role in talks to restore power-sharing.
Sir Malcolm has taken on a central role in the talks after nationalists and republicans questioned the impartiality of NI Secretary James Brokenshire.
Mr Sterling took control of Stormont's finances in March, due to a failure to pass a budget for the financial year.
He said that the civil service faced many challenges.
"I look forward to working closely with colleagues across all the departments to continue to deliver essential services for the people of Northern Ireland," he said.
"I will obviously be working very closely with Sir Malcolm over the next few weeks."
He has been using emergency powers to release cash and resources to departments until a new budget is in place.
Mr Sterling said that while the procedures could keep cash flowing to public services it was "not a substitute for a budget agreed by an executive".
David Sterling has been appointed as the new interim head of the Northern Ireland Civil Service.