Mhaissen, 31, is the founder and director of SDAID, an organisation that has since 2011 helped Syrians displaced by the war in their country and living as refugees in Lebanon.
"Rouba Mhaissen has contributed locally to improving the lives of people living as refugees in Lebanon in ways that protect their dignity and right to self-determination," the Rafto Foundation said in a statement.
Lebanon, which has four million inhabitants, says it has welcomed between 1.5 to 2 million Syrians, including one million listed as UN refugees, often living in precarious conditions.
In August, Amnesty International accused the country of "forcibly deporting" nearly 2,500 Syrians refugees back to their war-torn homeland.
Mhaissen is "a vocal and courageous front figure, speaking out against mounting pressure for the forced return of Syrian refugees, using insights and documentation of the experiences of those that have returned," the Rafto Foundation said.
The $20,000 (18,270-euro) prize will be formally presented to her at a ceremony in Bergen, in western Norway, on November 3.
Named after the late Norwegian human rights activist Thorolf Rafto, four past winners of the prize (Aung San Suu Kyi, Jose Ramos-Horta, Kim Dae-Jung and Shirin Ebadi) went on to win the Nobel Peace Prize, which is also awarded in Norway.
The Nobel laureate for 2019 will be announced on October 11.
Follow us on Twitter: @The_NewArab