While Jason Bartram will remain coach of the women's track endurance squad, Decker will now oversee those riders as well as the men's group.
Decker has enjoyed considerable success in charge of the men's track endurance program, which won silver in the team pursuit at the Rio Olympics.
The Australian team pursuiters broke the world record at last year's Commonwealth Games, going under three minutes 50 seconds for the first time, and have a fierce rivalry with the powerful British squad.
The men's team pursuit looms as one of Australian cycling's best chances for a gold medal at the Tokyo Olympics.
The world championships from February 27 to March 4 in Poland will give a clearer picture of where the men and women stand in the endurance events ahead of the Olympics.
Bartram took over the women's track endurance program two years ago after the controversial departure of veteran coach Gary Sutton, who now runs the same squad in the United States.
They were among several big changes early in the tenure of Cycling Australia performance director Simon Jones.
He said it made sense to have Decker overseeing the men's and women's track endurance squads.
"It's a little like what we've done on the road - we have one director leading a common approach," Jones said.
"It's a natural transition to align those programs, because it's much more efficient to have the groups frequently sharing the resources and knowledge.
"We do have limited resources, so that was as much about making sure that we gave the women the maximum support and also to create clear decision-making processes.
"Tim is the natural person to do that because of his experience."
The Americans are defending world champions in the women's team pursuit, although Australia did not compete in the event last year.
Australia only sent a skeleton team to last year's worlds, opting to focus instead on the Commonwealth Games.
"We feel we have some really, really opportunities in that women's endurance program," Jones said.
"It wasn't just about the short-term results, it is about the environment and sharing the knowledge."
Decker's portfolio was expanded before Christmas.
Australia will have a full-strength team at the Poland worlds.
"We're looking at six to eight genuine medal chances (in Olympic events)," Jones said.
The track endurance events on the Olympic program are the team pursuit, the madison and omnium.