Mohamed Zaree, who heads the Egypt country office of the Cairo Institute for Human Rights Studies (CIHRS), was hailed by the Martin Ennals Award organisers as a "hero".
Hans Thoolen, who created the prize in 1993 and chairs the jury, celebrated "the individual, heroic behaviour of this man, sitting all alone holding fort while the human rights situation around him is crumbling."
Zaree has remained in Cairo to continue defending freedom of expression and association in his country even after CIHRS had its assets frozen and was forced to move its headquarters to Tunis.
Zaree himself has faced death threats, been slapped with a travel ban since May 2016, and is awaiting a trial that could land him behind bars for life, CIHRS director Bahey El Din Hassan told reporters in Geneva ahead of Tuesday's award ceremony.
Zaree, who was barred from travelling to Switzerland for the event, was due to address the ceremony via video-link.
- 'Wake-up call' -
El Din Hassan said he hoped "the award would be a message, a wake-up call" to Egyptian President Abdel Fattah al-Sisi, warning the rights situation in the country was now worse than it was under Hosni Mubarak's 30-year regime, toppled in 2011.
Rights groups accuse the Egyptian government of arbitrary arrests and enforced disappearances of dissidents that spiked after the military overthrew Islamist president Mohamed Morsi in 2013 and cracked down on his supporters.
The government disputes such allegations.
Zaree has been charged under a law restricting foreign funding of civil society groups, and could face life in prison if found guilty of receiving funds from abroad, it said.
El Din Hassan slammed the international community for not speaking up more about the rights crackdown in Egypt.
"The silence is interpreted by the bloody dictators as greenlighting. So silence is not neutral. It is a green light" to continue abuses, he said.
Jury member Philip Lynch, who heads the International Service for Human Rights (ISHR) organisation, told reporters handing the prize to Zaree was not only to celebrate his achievements, but also a "collective condemnation ... of the Egyptian authorities' approach to human rights."
The jury expressed hope that the spotlight could offer protection to Zaree and other rights campaigners facing an increasingly hostile climate.
The other finalists for this year's prize were five Cambodian rights defenders known as the Khmer Five.
The five -- Ny Sokha, Yi Soksan, Nay Vanda, Lim Mony and Ny Chakrya -- have languished in pre-trial detention for the past year, facing charges linked to their work with the Cambodian Human Rights and Development Association (ADHOC).
This year's third finalist was Karla Avelar, a 39-year-old transgender woman who suffered horrific rape, abuse and violence.
Avelar, who helped found El Salvador's first association for trans people, and its first organisation for trans women with HIV.
The Martin Ennals foundation is named after the first secretary general of Amnesty International and the 30,000 Swiss franc ($30,000, 27,000 euros) prize is judged by the London-based rights group, along with Human Rights Watch and other leading organisations.
The other finalists were awarded 10,000 Swiss francs each from the foundation.
Last year's Martin Ennals laureate was Ilham Tohti, a jailed Chinese scholar defending the country's mostly-Muslim Uighur minority.