Dozens of photos and video popped up on social media showing dark clouds of smoke rising from the refinery, some with flames visible.
Litsa Daeres, who lives nearby, says she heard a "loud bang" and felt her whole house shake.
The refinery was operating under a shutdown, meaning there were more employees than usual working at the time of the accident.More news: What does the United Nations climate report say?
Saint John police said they are responding to an incident at the refinery and are asking residents to avoid the area altogether. "Praying for the safety of all involved".
They looked outside the window and saw black smoke and flames exceeding the height of the stacks at the refinery.
The refinery is near several residential neighbourhoods about five kilometres from the city core, known as Uptown.
Refinery owner Irving Oil confirmed on Twitter that a "major incident" occurred there.More news: Dana White Just Shared Some Major Conor McGregor News
Irving Oil says it is investigating a "major incident" at the refinery, but did not provide details. "At times we were letting that just safely extinguish itself", he said.
Dalzell, the chair of Saint John's Citizens Coalition for Clean Air, said the refinery already emits many different types of "volatile organic compounds" into the air: organic chemicals that have a high vapour pressure and can be hazardous to human health. "I heard a rumbling, roaring sound".
When he walked outside, he noticed black smoke coming from the refinery, so he hopped into the vehicle, drove down the corner and saw fire about 30 metres high.
We will update as more information becomes available.More news: Brett Kavanaugh a step closer to Supreme Court post
He made a decision to drive by the refinery, and said he was nearby when he felt the vibrations of what he assumed must be a second explosion.