"One moved to Amherst and one moved to Parrsboro ... I did miss them ... I had become quite good friends with them," Macgillivary told CBC News.
The school in the rural town of Advocate Harbour teaches classes from elementary school to high school and has a total of 60 students.
Although Macgillivary is the only senior, the school will still hold traditional senior class activities such as graduation and prom.
"Everything's going to play out just as usual as it always has," he told CTV News. "We're going to have a prom and a graduation; just I'm going to be the only graduate on stage during the time so it's going to be ... me."
Students from 6th to 12th grade will attend prom alongside Macgillivary and the entire school will participate in the graduation ceremony.
"It doesn't matter how many graduates there are. We're a small school, so we always make sure everybody is included in everything," Macgillivary said. "Everybody is very close to each other, everybody knows each other very well. We like to keep together."
A female student found herself in the same situation as Macgillivary three years ago and he reached out to her for advice before starting the year as the school's lone graduate.
"She said, 'Don't make yourself feel like you're alone. You have other students around to talk to and become close with so don't feel like you're all alone all the time. Talk to someone else," he said.
Macgillivary, who will serve as class valedictorian, said he felt nervous about speaking alone on stage in front of the entire school.
"It does feel weird. It's different knowing you're the only one everyone is going to be looking at," he said. "You're all alone, so everybody is looking at you and it is nerve-racking. There is no one there to take the attention off you ... but I'm ready for it."