Botswana's High Court, in a highly-anticipated verdict, on Tuesday ruled in favour of decriminalising homosexuality, which is outlawed under the country's 1965 penal code.
Judge Michael Elburu "set aside" the "provisions of a Victorian-era" and ordered the laws be amended.
In a courtroom packed with activists, the judge emphasised that the current laws oppressed a minority of the population.
"There’s nothing reasonable in discriminating," he said.
"We say the time has come that private, same sexuality must be decriminalized."
"It is a variety of human sexuality," he said.
The High Court had been petitioned by an anonymous person, identified only by initials LM for security reasons.
The individual challenged two sections of the penal code under which offenders face a jail sentence of up to seven years.
In March, the court postponed a ruling on the issue, sparking fears that the much-awaited decision could be delayed indefinitely.
But on Tuesday, Judge Elburu stressed that the country's highest judicial body took the matter deeply seriously.
"Sexual orientation is human, it's not a question of fashion," he said. "The question of private morality should not be the concerns of the law."
Last month, Kenya's High Court upheld laws against same-sex relations, dealing a blow to activists campaigning to roll back anti-gay laws and stigma in Africa.
Before Tuesday's ruling, 28 out of 49 countries in sub-Saharan Africa had laws penalising same-sex relationships, according to Neela Ghoshal, a Human Rights Watch (HRW) specialist in lesbian, gay, bisexual, and transgender rights.
The death penalty is on the books, under sharia, in Mauritania, Sudan and northern Nigeria, although there have been no known executions in recent times.
In southern Somalia, gay men are believed to have been put to death in territory ruled by the Al Shabaab jihadist group.
However, Angola, Mozambique and Seychelles have scrapped anti-gay laws in recent years.
Rights groups say many laws punishing homosexuality date from the colonial area.
They represent a peril even in countries where they are not implemented, according to campaigners, as their existence on the statute books entrenches discrimination and encourages harassment.
