Simmonds is poised for her fourth successive Games having already won eight medals, including five golds.
Stubbs was Paralympic champion in the individual compound event at Beijing 2008 and also claimed silver in the team compound at Rio 2016.
The pair will lead team-mates into the Olympic Stadium in the Japanese capital on Tuesday, with 12 days of action scheduled to begin the following day.
Simmonds, 26 is Great Britain' s first female flagbearer at a summer Paralympics since fellow swimmer Maggie McEleny in 2000.
"I'm hugely honoured to carry the flag for the ParalympicsGB team – on behalf of all the athletes, support staff and for the entire nation back home," she said in a statement.
"Just to be here in Tokyo is amazing but to carry the flag is the icing on the cake and I can't wait for the competition to start."
At the age of 56, Stubbs is the oldest athlete on the ParalympicsGB team.
He said: "I felt incredibly emotional when I was told the news. For any elite athlete to go to the Games and be bestowed this honour is a privilege. Words can't describe what it means to me.
"It's been a torrid year – unfortunately I lost my dad in January. He was my biggest fan, and hopefully if he's looking down on me, he's there saying: 'Do it for the Stubbs family John, you've earned it and you deserve it'. I know my family will be as proud as punch."
Meanwhile,the mood in the ParalympicsGB camp is "extraordinary" on the eve of the Tokyo 2020 Games, according to chef de mission Penny Briscoe.
A British team made up of 227 athletes across 19 of the 22 Paralympic sports are gearing up to begin competition in Japan after a challenging build-up severely affected by the coronavirus pandemic.
Briscoe said the athletes she has encountered cannot wait to get started.
"I think it's fair to say the mood in the camp is extraordinary. It's a mix of excitement, anticipation and elation," she said.
"The athletes are just pinching themselves. One of the shooters who has just landed said 'I didn't believe it until I touched down in Tokyo'.
"I think we're in good shape, and as a team we're really looking forward to the Tokyo 2020 Paralympic Games."
Sally Munday, the chief executive of the UK Sport agency which allocates funding to Olympic and Paralympic sports, backed the team to add to the feelgood factor generated by Team GB at the Olympic Games which ended earlier this month.
"We know that there's a glow that will already be around the British team that are there now in Tokyo and that the Paralympian delegation is going to create even more extraordinary moments to engage us as they prepare to realise their own dreams at the Games," she said.
"We also know that the journey to the start line for a lot of our athletes has not been easy.
"Whilst managing their own personal and sporting challenges, they've had extended periods of shielding and lack of competition because of the pandemic.
"Paralympians are all too aware of the challenges that we've all dealt with in the last 18 months, but it has impacted them in the most extraordinary way. But we know that they are here and ready now to make us all proud."