"I used to think whenever somebody was looking at me that [they thought] I am retarded or I'm an alien and look funny so I never wanted to leave the house," he said.
"I started playing up and being a rebel and was told to either leave or get expelled so I decided to leave."
He worked in racing stables before landing a work experience placement at Trinity Valley three years ago.
Trinity Valley owner Peter Townsend decided to employ him full time after a year of work experience.
"Since I've been working for Pete he has helped me so much. I was still nervous around everyone. I would go into the barn and hide.
"But Pete got me teaching a group of kids to ride and then from there I have just managed to talk to anyone."
Mr Flannagan said his employer had helped him overcome one of the biggest challenges he had faced at school - being able to socialise and feel accepted.
"At high school I used to walk around with my head looking at the ground, not acknowledging anyone. I was terrible with eye contact."
Mr Flannagan said he had grown from his position at the Trinity Valley Riding School as farm manager even though he had never had any formal training.
His duties included farm maintenance, including feeding watering and caring for the horses and helping out at the riding school.
Mr Flannagan said he loved his job.
Mr Flannagan, who admitted he initially thought horses were a "girly" thing, had also bought his own horse, Luna, and had been training her for a little over a year.
Mr Flannagan said he had no idea what he was doing when he first took her on but now the two had a special bond.
"Honestly, I feel they understand me better than humans. They are not judgmental either."
Farm owner Pete Townsend said Mr Flannagan was responsible for running the riding school.
"He would be a huge hole to fill now.
"He's got real good stickability and a real good way with them [horses], gentle and firm and the horses really respect him."
CCS Disability Action vocation services employment coordinator Lee Dickinson said Mr Flannagan was a young man made to feel quite worthless.
"But little by little he has put his shoulders back, his head up and has made himself and everybody else proud," she said.
Mr Flannagan said working on the horse farm he didn't feel like an outsider anymore and wanted to continue his career with training and riding horses on a national then international level "I actually feel important here."