Defence lawyer Ninetta Caparelli represented Boyle during his brief appearance Wednesday, and told court that going forward, Boyle will be represented by lawyers Lawrence Greenspon and Eric Granger.
With joint efforts by the United States and Canada, Boyle, his American wife, Caitlan Coleman, and their three children were brought back to Canada on October 13, 2017, five years after the couple were abducted by the Taliban-linked Haqqani network.
A publication ban bars reporting any information that could identify the alleged victims or witnesses in the case.
A senior official had said Boyle refused to board an American military plane after his rescue over concerns he could face arrest.
Joshua Boyle speaks to the media after arriving with his wife and three children to Toronto Pearson International Airport, almost 5 years after he and his wife were abducted in Afghanistan in 2012 by the Taliban-allied Haqqani network, in Toronto, Ontario, Canada, October 13, 2017. The couple were kidnapped while hiking in Afghanistan on their honeymoon in 2012, when Ms Coleman was five months pregnant.
Boyle said the child, named Marta Boyle, was killed "as retaliation" for his refusal to accept an unspecified offer by members of the terror group.
Joshua Boyle's long trip through the criminal justice system began Wednesday in a small Ottawa courtroom in a disturbing sex-crimes case that has drawn worldwide attention.
"Mr Boyle is presumed innocent of all charges".
Granger added: "He's never been in trouble before".
Joshua Boyle faces 15 charges, including sexual assualt, forcible confinement and uttering death threats. Pakistan's Foreign Ministry said the operation was based on a tip from USA intelligence.
According to the report, the alleged crimes took place in the city of Ottawa, and occurred between October 14 and December 30. She noted that she and their children were "healthy and holding up as well as we can". The Pakistanis caught the Haqqani fighters at some point after they had moved with their captives across the border from Afghanistan.
The family met with Prime Minister Justin Trudeau last month at his office on Parliament Hill and when asked for comment, a spokesperson for the Prime Minister's Office said only that "the prime minister did meet with them and confirmed it at the time".
A statement from Linda and Patrick Boyle on the release of their son Joshua, daughter-in-law Caitlan Coleman and their three grandchildren from the Taliban in Afghanistan.