The legislation would expand the Canadian Human Rights Act to cover transgender people.
The proposal would also amend the Criminal Code hate speech provisions to include transgender.
"I sincerely believe that in Canada we can and we should do more," Mr Trudeau said on Monday.
The Liberal government said the details of the legislation would be made public on Tuesday.
A similar measure was proposed in the House of Commons in 2011, but failed to pass the Senate.
Amanda Ryan, a transgender activist, told CTV that the move was welcome but largely symbolic because most Canadian provinces have enacted similar protection.
"It will have a strong psychological impact," Ms Ryan said.
The move comes as the issue of transgender rights has risen to prominence in the US.
On Friday in the US, President Barack Obama issued a sweeping order, saying transgender school pupils should be allowed to use toilets or changing rooms that match their gender identity.
A few US states have recently passed laws requiring transgender people to use public toilets that correspond to the sex listed on their birth certificate.
Mr Trudeau made the announcement after receiving the Laurent-McCutcheon Award, which honours advocates for gay rights.
His father, former Prime Minister Pierre Elliott Trudeau, posthumously received the same award in 2005 for de-criminalising homosexuality in 1969.
Mr Trudeau and his Liberal government have campaigned on a platform of expanding gay rights.
He plans to march in the Toronto Gay Pride parade in July, becoming one of the first world leaders to take part in such an event.
On Monday, Mr Trudeau said he would march in Montreal's parade as well.
Canadian Prime Minister Justin Trudeau plans to introduce legislation that would give broad legal protection to transgender people across Canada.