Blackburn was a four-year player for Notre Dame High School in Berlin, New Hampshire, and backstopped the team to four consecutive state tournaments. As a senior, Blackburn helped the team win the New England high school championship and was a star recruit for the University of New Hampshire in 1957. After a year on the freshman team Blackburn became the team's starting goaltender. New Hampshire was not among the elite eastern teams at the time: despite finishing with a 14–5 record, the Wildcats weren't considered for a postseason invitation, based on how weak their schedule was relative to other teams. Blackburn was one of the few highlights of the team during this time, and he was named team captain for his senior season. During his final year, the Wildcats produced a dreadful 3–11 record, with Blackburn surrendering over four goals a game. Despite the poor numbers, Rod was held in high regard both within the program and from outside sources. He was named an eastern All-American that season, becoming the first Wildcat so honored.
