In what's planned as an annual initiative, CA and most states/territories associations will fly the flag at their offices or grounds to honour the team.
Arriving in England on 13 May 1868, the Aboriginal team played 47 matches in five months abroad.
CA Chief Executive James Sutherland said the recognition date was another way Australian cricket could pay tribute to the courage of Australias first touring team.
"The 1868 Aboriginal tour of England marks an important event in Australias sporting and cricket history as the first cricket team to tour England," Sutherland said in a statement.
"The pioneering achievements of the 1868 team have in recent years started to become more widely acknowledged and celebrated, and we want that history and recognition to be ongoing.
"In 2002 Australian cricket was successful in having the team inducted into the Sport Australia Hall of Fame and in 2004, individual player numbers were allocated to the touring party as formal recognition of their place in Australian cricket history.
"Recognising May 13 each year was an idea suggested to us by one of our stakeholders and while its simple and easy to implement, it is a gesture of significance and another way we can keep raising awareness of crickets rich history and the contribution of indigenous players."
The aboriginal team played 47 matches between May and October 1868, winning 14 games, losing 14 and drawing 19.