Only Kagame and two other politicians – Frank Habineza of the Democratic Green Party and independent Philippe Mpayimana – were cleared by the electoral body.
Ms Rwigara, who was also disqualified from the 2017 poll, took to X, formerly Twitter, to express her disappointment to Mr Kagame.
“Why won’t you let me run? This is the second time you [have] cheat[ed] me out of my right to campaign,” she said.
The 42-year-old, who is the leader of the People Salvation Movement (PSM), had earlier told media-BBC’s Newsday programme that she had hoped to be able to stand this time round.
“Rwanda is portrayed as a country where the economy has been growing. But on the ground, it’s different. People do lack the basics of life, food, water, shelter.”
But on issuing its provisional list of candidates, the electoral commission said Ms Rwigara had failed to provide the correct documentation to show she had no criminal record.
It also said she had failed to show she had enough support nationwide to stand.
Another reason the commission gave was that Ms Rwigara had failed to prove she was Rwandan by birth. She once held Belgian citizenship but surrendered that in 2017 before her last bid to become a candidate.
But Ms Rwigara has told the BBC that she was born in Rwanda and dismissed all the other grounds for the rejection of her candidacy.
A total of nine applications to stand for president were received by Rwanda’s National Electoral Commission. Their final list will be announced next Friday as it still considering appeals lodged earlier in the process – though at this stage it is too late for the PSM leader to appeal.
In 2017 she was barred following accusations of forging the signatures of supporters for her application.
Ms Rwigara was imprisoned for more than a year but acquitted in 2018 over charges of inciting insurrection and forgery. She said the charges were politically motivated.
In March, a Rwandan court blocked efforts by prominent opposition figure Victoire Ingabire to lift a ban on her running in the presidential election.
She was freed in 2018 after spending eight years in prison for threatening state security and “belittling” the 1994 genocide.
In Rwanda, people who have been jailed for more than six months are barred from running in elections.
The two cleared candidates – Mr Habineza and Mr Mpayimana – were also the only candidates approved to stand against Mr Kagame in the 2017 election.
Mr Kagame is running for a fourth term, which could extend his presidency to nearly three decades should he win.
He won the last presidential election in 2017 with nearly 99% of the vote.
#BBC