The early monsoon has left more than 600 people dead in northern India, with more than 40,000 reported by the BBC to be stranded in the mountains of Uttarakhand state.
Four days of torrential rainfall triggered floodwaters and landslides in the state as well as parts of Nepal. As the monsoon rains came early, the region was "grossly" unprepared, GFA said.
The organisation has been meeting the basic needs of people on the periphery of the disaster zone and is awaiting the green light from the Indian government to enter the worst-hit areas.
"This suffering makes our hearts ache, because we know that God loves all of us," said KP Yohannan, GFA founder and president. "We must not only feel compassion, but we must also act to relieve suffering wherever we find it."
Thousands have been evacuated by the Indian government but with apartment buildings and homes washed away by the waters, officials have warned that the death toll could rise to 1,000.
A pastor in Saharanpur told GFA workers of people weeping as they watched their houses be washed away. GFA has been unable to contact some of its personnel in the worst-hit areas as power lines are down.
In Nepal, at least 39 people have been killed and GFA field reports put the number of people displaced from their homes there at over 2,000.
"Pray for the rescue of the missing and the stranded and that God would restore good weather in this area," said Yohannan. "In our Lord's name, we must pray and respond to this situation."
To donate to disaster relief in India and Nepal, visit www.gfa.org/flood/northindia/