The 31-year-old has announced he is hanging up his boots for good because of a knee problem.
Horn said the left-back’s decision was a massive blow – and described him as one of the best players he has ever worked with.
Brown began his career with Hearts and had spells with Livingston and Brechin City before joining Bonnyrigg in 2014.
He was already at New Dundas Park when Horn took over as manager. But the Rose boss was already fully aware from his own playing days of the ability of a player who represented Scotland at various age groups up top under-19.
Horn said: “When I came to Bonnyrigg I knew what I was getting.
"Johnny's a top, top player and if it hadn't been for injuries that he suffered when he was younger he probably would have played at a much higher level.
"Unfortunately he picked up a knee injury in our home game against Caley Braves last year. There was a hope that he maybe wouldn't require an operation but he is going to need one. There's a long waiting list and he’s got a young boy that he wants to kick a ball about with when he's older.
"It’s a really difficult decision for him to make . . . and a brave one.
"Since I've been at the club he's been absolutely fantastic. He's one of the best players I've worked with without a doubt.
"He’ll be a huge miss off the pitch as well. He keeps everybody going and is one of the leaders in the team so it's a massive blow.
"He's got to think about work commitments as well. He started a new job not all that long ago and it's not ideal for him if he's carrying an injury and sometimes his knee will just go
"He's a top lad who's been great for the football club and doesn't owe anybody anything at the club, that’s for sure. We wish him all the best ."
Announcing his retirement on Twitter, Brown said: “I’ve worked hard to try get back but operation is required.
"Hard decision but need to think about life outside of football and life with my son. Made mates for life and had some amazing times! Been a pleasure.”