The man in question, known only as A.I., arrived in Switzerland in 2012 and lodged an asylum request, the ECHR said in a press release.
He claimed that since secondary school he had been a member of a militant organization defending the rights of minorities in Darfur, Sudan. Since 2005 he had also been a member of armed opposition group the Justice and Equality Movement (JEM).
After being interviewed, the Swiss migration office (SEM) decided he did not meet the criteria of a refugee and therefore ordered him to be deported.
He then lost an appeal at the Swiss civil court before taking his case to the ECHR, claiming he ran a risk of being persecuted over his political activities if sent back.
In its judgement on Tuesday the ECHR said that “despite certain inconsistencies” there was no reason to doubt the credibility of his claims concerning his political activities.
It was not therefore unreasonable to think he was on the radar of the Sudanese intelligence services and consequently there were “reasonable grounds” to think he ran the risk of being detained, interrogated and tortured on his arrival at Khartoum airport.
Deporting him would violate articles three and two of the European Convention on Human Rights which ban torture and protect the right to life, it said.
In a second case related to another Sudanese man, the ECHR ruled in favour of Switzerland, saying the man, known as N.A., was not at risk of being tortured or ill-treated on his return.
The man, who also arrived in Switzerland in 2012, washed cars for a living and claimed to have been stopped and searching by the authorities for washing the car of a member of the JEM. He said he had been interrogated and ill-treated for 45 days and then imprisoned for five days.
But since his political activities in exile were limited he was not likely to be monitored by the Sudanese intelligence services, said the court.