The judge ruled that the government had acted unconstitutionally in blocking the group, Legabibo.
“I am happy with the judgement – it has sent a message to the government, the entire region and Africa,” the group’s Caine Youngman told the BBC.
Homosexual acts are illegal in Botswana, as in many African countries. The Botswana Penal Code, based on old English law, describes homosexual acts as offences against morality, punishable by up to seven years in prison.
“We are overjoyed at the outcome of the case. Lesbians, gays and bisexuals have long strived to be able to form an organisation which can support them and be their voice on matters that affect them,” said Mr Youngman.
The Southern Africa Litigation Centre (SALC), which often handles human rights cases across the region, said the ruling could have bigger implications.
“The judgment emphasises the importance of the rights to freedom of expressions, association and assembly in a democracy,” said SALC’s Anneke Meerkotter in a statement. “Importantly, the judgment emphasises that it is not a crime to be homosexual or attracted to someone of the same sex. The court finding is important not just for activists in Botswana but throughout Africa.”