The Scotland international initially joined the club as Assistant Coach in 2023, bringing a wealth of experience to the Myreside outfit thanks to his 61 caps for Scotland to date.
On his appointment Brown said: "I thoroughly enjoyed leading Watsonians forwards last year, leading an entire squad in a Head Coaching role is something I have wanted to do for a number of years.
"Watsonians have rich history of playing exciting and successful rugby at Myreside as one of Scotland's most successful clubs.
"There was real progress in the squad last year so now to be given the opportunity to take charge of the team for the next season is an honour, it's something I'm really excited about."