Governments are increasingly criminalising "homosexual acts" by seeking to impose new laws and draconian penalties, it adds.
This sends the "toxic message" that lesbian, gay, bisexual and transgender people are criminals, the report says.
Some of the continent's leaders say homosexuality is un-African.
In 2011, the US and UK hinted that they could withdraw from countries which did not respect homosexual rights on the socially conservative continent.
However, Amnesty said US religious groups "actively fund and promote homophobia in Africa", while many of the laws were inherited from the colonial era.
'Inflaming hostility'
Homosexual acts are still a crime in 38 sub-Saharan African countries it said in a report titled "Making Love a Crime: Criminalisation of same-sex conduct in sub-Saharan Africa".
There is no specific legislation outlawing homosexual acts in 12 African countries, mostly former French colonies, while gay rights are recognised in South Africa.
In the last five years, South Sudan and Burundi have introduced new laws criminalising same-sex relations, it says.
The parliaments of Uganda, Liberia and Nigeria have draft laws before them, seeking to increase penalties.
"These poisonous laws must be repealed and the human rights of all Africans upheld," Amnesty said.
"In some African countries political leaders target sexual orientation issues to distract attention from their overall human rights records, often marked by rampant discrimination and violence against women, corruption and lack of media freedoms," it added.
In South Africa, at least seven people, five of them lesbians, were murdered between June and November 2012 in what appears to have been targeted violence related to their sexual orientation or gender identity, the report says.
This is despite the fact that homosexual acts are not illegal in South Africa and the country boasts one of the most progressive constitutions in the world, it adds.
In many instances, media reports also inflame hostility towards people not conforming to heterosexual norms, Amnesty says.
In 2010, Uganda's Rolling Stone magazine published a photograph of gay rights activist David Kato next to a headline reading "Hang Them", it says.
Just a month later, he was killed in his home, although the police have denied it was a hate crime.
In Cameroon, people are regularly arrested after being denounced as being gay or lesbian because of their "appearance or conjecture, rather than evidence", Amnesty says.
Some individuals accused of same sex conduct in Cameroon have been imprisoned for three years without trial or charge, it adds.
Former detainees from Cameroon told Amnesty that they were subjected to "invasive procedures such as forced anal exams" while in custody, the report says.
In Kenya, people told Amnesty that sometimes the police threaten to arrest them under provisions in the penal code related to same-sex relations in order to obtain a bribe, the report adds.
"Extortionists also use the existence of these laws to demand money or goods in exchange for not revealing real or even made-up private details to the media, community or police," Amnesty said.
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