The 57-year-old, who served in the military for 33 years to attain the rank of lieutenant general and head the Defense Intelligence Agency, served as Trump's leading adviser on national security issues during the campaign.
An early supporter of Trump, Flynn was also a vocal critic of Clinton. At the Republican National Convention in July, he chanted "lock her up" with the crowd, an oft-heard slogan at Trump campaign rallies calling for Clinton to be put in jail over her use of a private email server for official communications.
Flynn's fiery rhetoric, in addition to his hardline stance on radical Islam and torture, led many to view him as a controversial campaign adviser.
However, Flynn's controversial standing may not matter much, as the national security adviser does not require Senate confirmation.
What does the national security adviser do?
The person appointed to this cabinet post "advises the president on issues linked to foreign affairs, security and defence," explains Laurence Nardon, researcher at the French Institute of International Relations.
"The role of the national security adviser is very important. He or she heads the National Security Council, which is a unit within the White House administration."
She adds that the national security adviser is "as powerful as the Secretary of State or Secretary of Defense" within a presidential administration.
Islam a 'political ideology'
Flynn has strongly criticised President Barack Obama's foreign policy in relation to fighting terrorism.
"Because of Obama's ill-advised actions, the world has lost American leadership," he told the crowd at July's Republican National Convention.
At another event in Texas this past summer, organised by conservative national security group ACT for America, Flynn said that Islam will "mask itself as a religion globally, especially in the West and especially in the United States".
"I don't see Islam as a religion. I see it as a political ideology," he added.
This view differs markedly from that of the Obama administration, which means that, if Flynn accepts Trump's offer, we could expect to see a number of foreign policy changes.
If Flynn accepts the position, there will be a shift in US foreign policy "to view the threat of radical Islam much more seriously than has been the case under President Obama", says Svante Cornell, cofounder and Director of the Institute for Security and Development Policy,
"A lot of other issues on the international agenda would be seen within that prism," he adds.
Russia is a particular sticking point between Flynn and Republicans in Washington, as they have "dramatically diverging analyses" on the issue.
"Mr Flynn appears to see Russia as an ally against the main threat of radical Islam, while many others in the Republican Party and the military establishment, quite to the contrary, see Russia as a larger threat to the United States' national security interests."