A three-judge court in Kigali acquitted Christopher Kayumba of all charges on Wednesday, ruling that the evidence presented by the prosecution "is insufficient".
"Court finds Dr. Kayumba not guilty on all the charges and orders for his immediate release," the court ruled.
Kayumba was arrested in September 2021 after the allegations were made by several people, including a former student, according to the Rwanda Investigation Bureau (RIB).
Shortly afterwards, allegations of rape surfaced against him on social networks and he denied them.
He was arrested and charged with rape and complicity to rape.
Prosecutors had sought a 10-year jail term.
Kayumba, who has been in detention with no bail, in 2021 launched a hunger strike to protest against the "politically motivated" charges.
The former Kigali journalism school lecturer ended the hunger strike after 11 days due to a "diabetic condition that had deteriorated quickly and put his life in danger", his lawyer said.
In December 2019, Kayumba was arrested and sentenced to a year in jail for "public disturbance" after airport security refused to allow him to travel to Nairobi.
The authorities said he had appeared at the airport late and drunk and had threatened to shut down the facility.
Rwanda, ruled by Paul Kagame since the end of the 1994 genocide which left some 800,000 Tutsis and moderate Hutus dead, has often come under fire for rights abuses and a crackdown on freedom of speech, critics and the opposition.
Rights groups have voiced alarm over Kigali's crackdown, including on people using YouTube or blogs to speak out about sometimes controversial issues in Rwanda.
A man in charge of recruitment in the group Kayumba set up was sentenced last year to 10 years in prison for forming a criminal organization.