A fierce critic of Rwanda's long-ruling President Paul Kagame, Ingabire spent eight years in prison before receiving a presidential pardon in 2018 that cut short her 15-year sentence.
She had asked the Kigali high court to remove her convictions, which would allow her to contest the July 15 polls despite a legal ban on convicted candidates who have been jailed for six months or longer.
"The court finds that Ingabire's request to have her conviction removed is not accepted," a judge said, reading out the decision.
"The court finds that in (the) presidential pardon granted to Ingabire, there were conditions that were set that she must follow," the judge said, adding, "therefore her appeal has no basis."
"I disagree with this ruling. It is clearly politicised. We still have a country where the courts are still not independent," Ingabire told AFP after the court decision.
According to Rwandan law, she will be allowed to appeal the ruling only after two years.
The polls are widely expected to return Kagame to office for a fourth seven-year term, after he presided over controversial constitution amendments allowing him to potentially rule until 2034.
The 66-year-old has been at the helm of the landlocked African nation for decades, winning presidential elections in 2003, 2010 and 2017 — with more than 90 percent of the vote.
Kagame's only known challenger in the July polls is Green Party leader Frank Habineza, who secured 0.45 percent of the vote in 2017. All other legally registered opposition parties back the ruling Rwandan Patriotic Front.
Ingabire's Dalfa Umurinzi (Development And Liberty For All) movement is not officially registered in Rwanda.
An ethnic Hutu, Ingabire, 55, was accused of "divisionism" after publicly questioning the government narrative of the 1994 genocide targeting the Tutsi minority that killed around 800,000 people.
Kagame has been praised for bringing stability to the African nation but his government's dismal human rights record has drawn censure.
'Urgent need for reform'
In a statement published on social media after Wednesday's verdict, Ingabire said the ruling "is not merely a personal setback but is emblematic of the broader issues facing our nation."
"Today's decision is a stark reminder of the barriers to political participation and the urgent need for reform in our country's governance."
Ingabire regularly accuses the Rwandan leader of suppressing dissent and neglecting the poor.
Following her 2018 release from jail, she had told reporters she was freed because of international pressure on Rwanda's government, prompting a warning from Kagame: "Do not be shocked if you go back to prison."
Numerous opposition politicians have disappeared or been killed in mysterious circumstances over the last few years.
A member of Ingabire's former party FDU-Inkingi was stabbed near the capital Kigali in September 2019, six months after the party's spokesman Anselm Mutuyimana was kidnapped and his body later found in a forest.
Based in The Netherlands since 1994, Ingabire returned to Rwanda in 2010, intending to run for president as FDU-Inkingi's leader.
But she was arrested after calling for perpetrators of crimes against the Hutu majority also to be pursued and punished.
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