2010-11: Phil Baltisberger played five games in Switzerland U20 junior hockey as a 15-year old and was an assistant captain for ZSC's U17 team in the Swiss Elite Novizen. He played in international competition at the U19, U17, and U16 levels. Baltisberger had 1 assist with the GCK Lions in his only Elite Junior A league game. He scored 1 goal with 1 assist in three regular season games and had 1 assist and 2 penalty minutes in one playoff game for ZSC's Elite Junior B champion team. Baltisberger scored 6 goals with 14 assists and 63 penalty minutes for the ZSC U17 team in 31 regular season games and had 4 assists and 16 penalty minutes in eight playoff games. He was scoreless in his only game with Switzerland's U19 team, had 1 assist in three games with the U17 team and in 11 games with Switzerland's U16 team he scored 1 goal with 31 penalty minutes.
2011-12: Baltisberger spent most of the season playing against professionals and skated for Switzerland's U20 and U18 teams. He appeared in one National A League playoff game with ZSC with no points nor penalties, and played 41 games for GC Kusnacht Lions in the National B League. Baltisberger scored 1 goal with 2 assists and 20 penalty minutes in 36 regular season games and had no points and 4 penalty minutes in five National B playoff games. He was -2 with no points in six games as Switzerland finished eighth in the 2012 WJC U20 tournament in Canada. He had 1 assist and was +1 with 4 penalty minutes in four games for Switzerland's U18 team at the 2011 Ivan Hlinka Memorial Tournament and was -2 with 1 assist and 8 penalty minutes as the Swiss finished in 11th place at the WJC U18 tournament. Baltisberger played for the GCK Lions U20 team during its playoff championship run; scoring 1 goal with 2 assists and 10 penalty minutes in seven playoff games. He was selected by Yugra-Khanty-Mansiysk in the second round (41st overall) of the 2012 KHL Draft.
2012-13: Baltisberger saw action in five games with ZSC the National A playoffs with after skating for the GCK Lions in the National B league during the year and won a second straight Elite Junior A title with the Lions' U20 team. He appeared in his second World Junior Championship tournament for Switzerland's U20 team. Baltisberger played in the 2012 Ivan Hlinka Memorial Tournament and was a team captain at the 2013 WJC with the Swiss U18 team. He was -1 with no points nor penalty minutes with ZSC. In 39 regular season National B games he scored 2 goals with 12 assists and 48 penalty minutes. He scored 2 goals with 4 penalty minutes in four playoff games for the Lions. Baltisberger had 1 assist and an even plus/minus as Switzerland finished sixth at the U20 WJC in Ufa, Russia. He scored 1 goal with 3 assists in four games at the Ivan Hlinka tournament and scored 1 goal with 3 assists in five games and was -5 with 2 penalty minutes as Switzerland finished sixth in the WJC U18 tournament in Sochi. In 10 games with GCK Lions during the Elite Junior A playoffs Baltisberger scored 2 goals with 5 assists and 14 penalty minutes. Guelph selected him in the first round (26th overall) of the 2013 CHL Import Draft.
2013-14: Baltisberger played for the OHL champion Guelph Storm in his first season in North America and represented Switzerland in the 2014 World Junior Championship in Malmo, Sweden. He scored 1 goal with 14 assists and was +25 with 36 penalty minutes in 57 games for Guelph during the regular season. The Storm had the OHL's best record — finishing first in the Midwest Division — and defeated North Bay in five games in a best-of-seven series in the OHL finals to advance to the Memorial Cup. Baltisberger scored 2 goals with 3 assists and was +18 with 20 penalty minutes in 20 OHL playoff games. He was ranked 197th amongst North American skaters in Central Scouting's final rankings prior to the 2014 NHL Draft.