"It think it's going to be really good for customers," she said.
Mr Duncan said they were approached by The Chemists, which is located one shop away on Queen St, about the merger late last year.
Queen Street Pharmacy will move into The Chemists premises and trade as The Chemists from February 1.
He said the decision to merge was made in weeks rather than months, and they planned to keep most, if not all, staff employed.
Mrs Duncan said the move was bittersweet but they and the staff were excited about the change.
"I think it's making the best of a bad situation ... but it is exciting," Mrs Duncan said.
"It's going to be sad to close the doors on this shop."
Queen Street Pharmacy was set up after the closure of The Chapel Street Family Doctors in 2010.
The couple said most of their regular customers had followed them to Queen Street Pharmacy and they were hoping they would move with them again.
This would also be the first time The Chemists would be under local ownership in 10 years.
"We're really excited to bring it back to Masterton ownership," said Mr Duncan.
The Chemists and Queen Street Pharmacy will close early at 3pm on January 31 to transfer computer records and stock, and the combined business will reopen the next day.
Queen Street Pharmacy customers should note that all repeats, prescriptions and blister packs would be moved to The Chemists and will be available as usual.