The alerts will provide all available details of the missing child and can be easily shared, to help spread the word.
The social media network says it will work with police in major centres across the country to get the alerts out.
Facebook started a similar system in the United States in January.
Public Safety Minister Steven Blaney made the announcement today at Ottawa police headquarters.
Blaney says the project will mobilize the online community in the event of an abduction.
He pointed out that Monday was National Missing Children's Day.
"There is no greater fear for a parent than the possibility of a missing child," he said in a statement.
"Today is an important day to remember not only children who have gone missing, but also their loved ones."
Jordan Banks, managing director of Facebook Canada, said speed is vital in dealing with an abduction.
"The most valuable thing we can do is get information out to the public as fast as possible," he said in a statement.
"By getting the right information to the right people at the right time through targeted Amber alerts on Facebook, we hope to reunite missing children with their families faster."
Pina Arcamone, director general of the Missing Children's Network, said Facebook is uniquely positioned to help with Amber Alerts.
"When a child disappears, every second counts and statistics have shown that the rapid dissemination of information greatly increases the chances of locating a missing child, safe and sound. Facebook's geo-targeted alerts will give Amber alerts an expanded social media and Internet presence, thus greatly enhancing our abilities to quickly recover the child."
Last year, a newborn abducted from a hospital in Trois-Rivieres, Que., was found after four teens saw a photo of the suspect in their news feeds and recognized her.