Starting on the back nine, Prayad sunk a 30-foot birdie on his first hole of the day and then picked up another shot at the next to boost his chances of reclaiming the trophy he won in 2013.
The 49-year-old Thai moved to eight-under with Canadian Richard Lee two shots adrift in second after a round of 67.
Overnight leader Atthaphon Sriboonkaew (71) of Thailand, compatriot Thaworn Wiratchant (68) and Japanese Akinori Tani, who will return on Saturday to finish his round, were a shot further behind.
Play resumed after a two-hour rain delay at the Santiburi Samui Country Club and 31 players will resume their second rounds on Saturday morning, Asian Tour organisers said.
Prayad, an eight-time Asian Tour winner, had finished his first round with three consecutive birdies and started his second round where he left off on Thursday.
"I got off to a solid start. Before the round, I told myself it does not matter who is leading, as long as it's a Thai player, I am OK with it," he said.
"I didn't expect myself to lead now but it's always good coming back to play here. I like this course a lot and playing this week brings back a lot of memories from my win in 2013.
"I putted so well. I made a couple of long putts. Hopefully I can keep the trophy on home soil this week."
Thaworn also hopes to stay in contention for the $300,000 event, staged in honour of Thailand's Queen Sirikit.
"I played good today, given the tough conditions out there. I am happy with where I stand at the moment and I believe I still have the chance to break my own records this week," said Thaworn, who has a record 18 titles on the Asian Tour.
(Writing by Sudipto Ganguly in Mumbai; editing by Toby Davis)
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