Mr Morgan, who joined the trust temporarily from Lincolnshire Community Health Services NHS Trust last July, said there was still work to do.
He will continue in the role at ULHT until March 2022.
The trust finds itself in both financial and quality special measures and has struggled recently with soaring demand at its emergency departments.
Mr Morgan said when he took the position that he intended to “bat for Lincolnshire” and fight for his “fair share of the national cake” for more funding for the county.
He tweeted this morning that, while he was pleased to carry on as CEO, there was more to do.
“I have agreed to extend my secondment as ULHT CEO until the end of March 2022,” he said.
“Absolutely delighted. Lots to be done but our fantastic people will make that happen.”
The trust requires around £20 million to extend Lincoln A&E due to “significant pressure” on the department.
It follows the significant pressure at the county’s emergency departments in recent months.
Shortly after taking the role, Mr Morgan welcomed an announcement from the government that £21 million would be provided to increase Boston Pilgrim A&E’s capacity.
Mr Morgan said he would use any means necessary to lobby for further funding.
“I want a big share of the national cake as I can get my hands on and I will use MPs, county council and anyone else I can speak to to lobby for my share as I would see it of that national cake,” he said.