The Aberdeen South MP labelled reports he was uncomfortable with the idea as “nonsense” and stressed he could not wait to learn from “Europe’s most successful politician” in Ms Sturgeon.
Speaking exclusively to The Scotsman, Mr Flynn added his party was united, despite claims of a rift after he replaced Ian Blackford earlier this month, with Mhairi Black taking over as deputy leader.
Asked about his relationship with the First Minister, Mr Flynn said “of course” the pair talk.
He said: “I've seen these stories as well. They are complete and utter nonsense. I am genuinely excited to be in a position where Mhairi Black and I can work with the most successful politician in Europe and hopefully we can work with her and learn from her.
"The SNP is very much united on these issues, no matter some of the content out there. There is no big split or determination to do anything ad-hoc."
Quizzed on a timetable for a second vote on Scottish independence, Mr Flynn explained things would be clearer after his party held a special conference on the issue in the new year.
The SNP will hold a special one-day conference on March 19 next year to decide "the way forward to secure independence".
It follows the UK Supreme Court ruling that Holyrood does not have the power to stage another referendum – a judgement that prompted Ms Sturgeon to vow to push ahead with the “de-facto” referendum plans to try to win independence.
Mr Flynn said: “We are going into party conference in the new year and we’ll be putting the meat and bones onto our de-facto referendum position, which I fully support by the way.
“Opposition parties have no interest in respecting the rights of the people of Scotland to determine their own future and we need to work around that, and make sure we take people with us.
“Democracy matters. We’ve seen with Brexit how our democracy and our views have been ignored. The UK is not a union of equals in the way it has been sold to people in the past.
“The importance of democracy will hit home with those who may not be fervently in favour of independence yet.”
Since taking over, Mr Flynn has already turned heads for his performances at Prime Minister’s Questions, where he forgoes notes and asks questions from memory – something he admits makes him “nervous”.
He said: “I’m worried every time I go to speak in the chamber. It’s natural, we’ve all got an element of imposter syndrome, especially when it comes to Westminster, when you’re surrounded by people from very different backgrounds to yourself.
“[Without notes is] how I like to approach it. I read a lot and like to talk about the big issues of the day.
“It’s more engaging for people watching. I’m very much about politics that will make people sit up and listen.”
However, there have been rumblings of dissent among Mr Flynn’s MPs, with anonymous briefings and questions as to why a change in leadership was required.
Insisting he only stood when it was clear Mr Blackford was standing down, the history and politics graduate said he would bring a change of approach.
Mr Flynn said: “I’m quite assertive, quite energetic and passionate about the subject matters I speak about. Same applies for Mhairi, so hopefully together we can take that into the chamber and communities right across Scotland.
“We want to get folk up for the campaign to come and that’s at the forefront of my thoughts, Mhairi, and all my colleagues’ thoughts, to drive that home while at the same time holding this [UK] Government to account."
His approach has also seen a refocused attack on Labour, with Sir Keir Starmer’s party criticised in his both of Mr Flynn’s PMQs appearances to date.
Asked about whether this represented a new tactic, Mr Flynn insisted he was just “stating the obvious”.
He said: “The Labour party when it comes to Brexit, migration, democracy, they are very much mores closely aligned to the Conservative than they’ve ever been, and I think it’s important that folk know about that.
"I think it’s all good and well calling out the UK Government and its failings, but the reality is that the alternative is Keir Starmer. The narrative Keir Starmer has put forward on the big issues of the day are not in line with my views and i don’t think the views of Scotland.
“On some stuff, like Brexit and asylum seekers, I don’t think even Keir Starmer believes what he says.”
It comes as support for independence surges, with six successive polls putting Yes ahead since the Supreme Court’s decision on November 23.
The first time polling companies have given Yes a lead in two years, the survey outcomes have prompted polling expert Sir John Curtice to conclude that just saying “no” to another referendum was no longer “a viable long-term strategy for maintaining public support for the Union”.
However, the SNP Westminster leadership still feels there is more to do, with Ms Black telling sister title Scotland on Sunday her party must do more to explain why they want Scotland to be independent.
Agreeing, Mr Flynn said he wanted the polls to continue to grow and his colleagues to keeping making a “positive” case for independence.
He said: “I think we all are aware of the fact we are in a fantastic position in the polls, but what I want to see is us get to a point where those polls are maintained, where those polls rise. The way to achieve that is to make a positive case for independence.
“The situation in Westminster is unsustainable, on migration, Brexit, the economy, but also just in terms of democracy. The two main parties are so disconnected from where we are and the people of Scotland.
“I agree with what she [Ms Black] said. The Scottish Government has put out some independence papers that have been excellent so far, and I’m really excited about them.
“They provide the platform for that discussion about what independence can actually mean, having complete control of your economy, full power in a Parliament and that is an exciting conversation to have."
The 34-year-old also revealed he was upset by his public portrayal as a “beer-swigging” lad, due to his apparent membership of the “Tuesday Club” – a five-a-side football gathering that reports claimed met with the aim of ousting his predecessor.
Mr Flynn insisted it was purely social, adding he didn’t even like curry. He said: “It is genuinely frustrating and upset me at points, it could not be further from the truth.
“My cardinal sin is that I once a month as a former disabled person who didn’t get to play football for some time occasionally did do just that.
“The narrative that has been built around myself and some of my colleagues, if the biggest crime they’ve committed is playing football and trying to have a bit of camaraderie whilst we’re in London, that’s a sad state of affairs.
“I’d add that politicians in other parties all play football, including Keir Starmer. It’s just been blown out of all proportion, it’s a load of nonsense.”