In a statement on Wednesday morning, Ms Fitzharris said she would step down as transport and health minister on July 1, before leaving the Assembly entirely in the coming weeks.

Ms Fitzharris has been the territory's health and transport minister since 2016, during a transformative and at times controversial period.

She has overseen the delivery of light rail stage one, the territory's biggest ever infrastructure project.

During her tenure as Health Minister, the department has been plagued with deep performance and cultural issues.

ACT's hospitals have consistently performed poorly in key national performance indicators including emergency department and elective surgery wait times.

Last year, Ms Fitzharris oversaw an independent review into ACT's public health system's culture, following months of building pressure and allegations of widespread bullying.

An overhaul to the bus system earlier this year caused an outpouring of negative reactions, with Ms Fitzharris revealing last week the government had received thousands of complaints about it.

Ms Fitzharris held a press conference this morning alongside Chief Minister Andrew Barr regarding her resignation. The Canberra Times was not invited.

In her statement, Ms Fitzharris said her decision to step down was a personal one, stemming from a desire to better balance her family life.

"This has been an incredibly difficult decision for me, but it is the right decision and will allow a new member of our team to come into the Assembly prior to the 2020 election," it read.

"I hope to continue to make a contribution to our amazing city in life after politics. I will continue to be a working mum, something my husband and I have balanced since each of our children were born. Now is the time for a new balance and new opportunities.

"And I hope that other working mums and dads - indeed people of all ages and backgrounds - consider running for public office. It is an important role; and it is more than a job."

Ms Fitzharris entered the Assembly in 2015, filling a position vacated by former chief minister Katy Gallagher.

Ms Fitzharris took on the transport, health and higher education portfolios in 2016, as she quickly rose to become one of the most senior members of chief minister Andrew Barr's cabinet.

She is expected to be replaced by Deepak-Raj Gupta in the Yerrabi electorate, who on Wednesday said he would accept the position.

In the event of mid-term resignations, ACT parliamentarians are elected by a countback of votes at the last election.

Mr Gupta, 52, is a leader in the Indian community in Gungahlin and a public servant. Factionally unaligned, Mr Gupta's election will shift the factional balance within the Labor government, undermining Mr Barr's grip on power.

Ms Fitzharris was a senior member of the Labor right, and has long been considered as a natural successor to Mr Barr. With the department of Ms Fitzharris, and assuming Mr Gupta is elected, Labor's right faction will have just four members in the Assembly.

On Wednesday, Mr Barr said Ms Fitzharris role in steering the delivery of light rail would be part of her "impressive legacy as a MLA for decades to come".

"Ministers in the ACT Government take on huge responsibilities, and at times these come at a cost to our personal lives," Mr Barr said.

"I understand Meegan's decision and I wish her and her family the best in life after politics. Personally, I have always valued Meegan's advice and support throughout her time as an MLA."

Mr Barr said the health, transport and higher education portfolios would be shifted to other ministers in the short term, with a wider cabinet reshuffle set for later in the year.

Deputy Chief Minister Yvette Berry said Ms Fitzharris' departure was a "big loss to the government and the Canberra community".

"Meegan and I have been friends through our time in the Assembly, as mums and ministers with all that brings. We both put our hands up for election because we care deeply about our communities and I've got no doubt her passion and advocacy for Gungahlin will carry on into the future," Ms Berry said.

"These jobs don't make much allowance for personal lives. Although I'll miss her she has made her decision and I respect that."

Opposition leader Alistair Coe said Ms Fitzharris had been a strong local member and a prominent minister in the government.

"During her time in the Assembly, in addition to being a local member, she has presided over construction of the light rail project and many changes in the health system," he said.

"Her workload, particularly in the health portfolio, was extremely challenging yet she was always professional and committed to her duties.

"Life in public office demands long hours and personal sacrifices. I thank her and her family for all that they have contributed to the Territory.

"She has been a strong local Member and prominent Minister in the Government.

"I wish her and her family all the best for the next stage in their journey."

Acting Greens leader Caroline Le Couteur said Ms Fitzharris had made a "positive contribution" to the national capital.

"We have had a good working relationship with Minister Fitzharris and appreciate that she has been a hardworking, cooperative and positive member of the Assembly," Ms Le Couteur said.