The goal is part of the company's climate change strategy and will be underpinned by a commitment to reduce scope 1 and 2 emissions from existing operations by 26% by 2030.
"Fortescue has a proud history of setting stretch targets and our 2030 emissions reduction commitment, together with our goal to achieve net zero operational emissions by 2040, positions Fortescue as a leader in addressing the global climate change challenge," CEO Elizabeth Gaines said.
"Fortescue supports the Paris Agreement long-term goal of limiting global temperature rise to well below 2°C above pre-industrial levels, and our emissions reduction targets align with this international objective.
"Our success will be founded on practical initiatives that will allow us to deliver on our targets in an economically sustainable manner."
FMG and its partners have announced investments of more than US$800 million in energy infrastructure projects, including the Chichester solar gas hybrid project and the $700 million Pilbara Energy Connect project.
The company has also partnered with CSIRO to develop metal membrane technology, which provides the potential for the bulk transportation of hydrogen through ammonia.
"Mining is one of the most innovative industries in the world and Fortescue is harnessing this technology and capability to achieve carbon neutrality with a sense of urgency," Gaines said.
"In addition to the development of gas technology and renewables for our stationary energy requirements, we are working towards decarbonising our mobile fleet through the next phase of hydrogen and battery electric energy solutions."
FMG follows other major mining companies in setting an emissions target.
In mid-2019, BHP set a target of net zero emissions by 2050, while Rio Tinto followed with the same target earlier this year.
Vale and Teck Resources also have both recently set targets to be carbon-neutral by 2050.
Anglo American has a vision to achieve carbon neutral mining by 2040.
The industry is still split on scope 3 emissions, being the emissions emitted by miners' customers.
BHP and Anglo have committed to reduce scope 3 emissions, while Rio and FMG have stood firm, saying they cannot control the actions of their customers.