2009-10: Rupert skated in four junior A games with the Greater Ontario Junior Hockey League's Lambton Shores Predators and was one of the top scorers for the Elgin Middlesex Chiefs minor midget AAA team. He had 2 assists and 12 penalty minutes in his brief time with the Predators. Skating alongside his twin brother Matt Rupert on the Chiefs, Ryan scored 22 goals with 27 assists and had 40 penalty minutes in 30 games. In 15 playoff games he scored 11 goals with 10 assists and had 22 penalty minutes. Ryan Ruppert was selected by London in the third round (49th overall) of the 2010 OHL Priority Draft.
2010-11: Both Ryan and Matt Rupert split the season between the OHL's London Knights and Lambton Shores in the GOJHL. In 39 regular season games with the Knights, Ryan Rupert scored 9 goals with 18 assists and was plus-two with 30 penalty minutes. He skated in all six playoff games during the Knights' series with Owen Sound and was minus-four with 2 goals and1 assist and had 6 penalty minutes. In 25 games with the Predators he scored 15 goals with 21 assists and had 107 penalty minutes.
2011-12: Rupert skated in 63 of 68 games for London in his first full OHL season – missing five games due to a suspension he received in November for a post-game altercation. Rupert displayed both playmaking ability and an edge to his game – finishing plus-10 with 17 goals and 31 assists and leading the Knights with 120 penalty minutes. The Knights finished first in the Midwest Division and reached the Memorial Cup after winning the OHL playoff title. In 19 OHL playoff games Rupert scored 9 goals with 6 assists and was plus-five with 31 penalty minutes. Rupert was the second-leading scorer for London in the Memorial Cup behind Nashville prospect Austin Watson. In four games he scored 2 goals with 1 assist and was an even plus/minus with 8 penalty minutes. London lost to Shawinigan, 2-1 in overtime, in the championship game. Not among the 210 North American skaters listed in Central Scouting's final rankings prior to the 2012 NHL Draft, Rupert was selected by Toronto in the sixth round (157th overall).