Auburn Doubledays
The Toronto Blue Jays selected Wojciechowski in the first round, with the 41st overall selection, of the 2010 Major League Baseball draft. He received an $815,000 signing bonus, and made his professional debut with the Auburn Doubledays of the Class A-Short Season New York–Penn League. In 2011, Wojciechowski played for the Dunedin Blue Jays of the Class A-Advanced Florida State League. The Blue Jays assigned Wojciechowski to Dunedin in 2012.