Michael Lebruru, one of three investigating judges, said sections 164 and 165 of the penal code undermined a person's right to dignity, privacy and freedom, and were discriminatory.
The court in the capital Gaborone overturned the two sections, in force since 1964, which criminalized "carnal knowledge of any person against the order of nature" and "unnatural offences," respectively, Efe news reported.
"Public opinion in cases like this is relevant but not decisive," Leburu said, adding: "This is about fundamental rights more than the public's view."
The complainants had requested a revision of the constitutionality of the laws criminalizing sexual relations between people of the same sex.
"The state cannot be sheriff in people's bedroom," the judge said.
Having same-sex relations in Botswana was punishable by up to seven years in prison.
The judge said a democratic country practices tolerance, diversity and mental openness, adding that social inclusion is paramount to ending poverty and reaching shared prosperity.
Botswana joins 21 African countries, among them Rwanda, Ivory Coast and the Seychelles, that do not criminalize sexual relations between same-sex couples.
The ruling was good news for the LGBT community in Africa after Kenya's Supreme Court in Nairobi recently upheld articles criminalizing gay sex in that country.
Members of the LGBT community who were present in Botswana on Tuesday left the courtroom visibly content with the ruling, while social networks were filled with messages of congratulations.
( With inputs from IANS )