Johnstone, who left the school 17 years ago, was not far from the thoughts of Outram Primary School pupil Brooke McAlwee (12), who organised for every pupil to write a message to him before the Rio Olympics.
''I just thought it was important for Clarke to know that we were backing him,'' Brooke said.
Johnstone said his parents delivered the book containing the pupils' messages to him a few days before he competed in Rio.
''It was a lovely surprise.''
Johnstone was greeted by wide eyes and smiles when he surprised about 180 Outram Primary School pupils at their morning assembly.
''It was incredible, certainly the highlight of my life so far,'' Johnstone said of the Olympic experience.
''It was frustrating and slightly heartbreaking to miss a medal by the smallest of margins, though.''
New Zealand finished fourth.
Johnstone felt excited to return to his former school where he spent much of his time playing sports. However, riding was not one of them.
''I gave everything a try. I wasn't that good at some things.
''It wasn't until I started riding I found something I excelled at.''
Johnstone was bombarded by questions from pupils.
He said he was pleased with his performance in the team event. However, the worst experience was Sir Mark Todd's disappointing showjumping round.
Johnstone said the school had changed since he was a pupil there. However, one of his ''favourite'' teachers, Janferie Tansley, still taught there.
At the assembly, Ms Tansley reminded Johnstone he had not shown a particular passion for riding while attending the school.
''You are a really good example of someone at that age that didn't have that passion yet but developed it and went very far.''
Johnstone said although he did not leave the Games with a medal he was the only person in the equestrian team to have received a book from their former primary school.
''That was a really, really lovely thing for you guys to do.''
