Christopher Fuss, 46, from Glengowrie in Adelaide's inner west, was remanded in custody last month after appearing in the Adelaide Magistrates Court charged with five counts of dishonestly taking property without owner's consent.

The alleged theft of $20.5 million occurred between October 31, 2009 and January 20, 2010.

Today, Flinders University announced the court's decision to order the return on $13.9 million.

"The university is actively seeking restitution of all of the misappropriated funds as soon as possible and the court ordered transfer is the first step towards that goal," the university said in a statement.

The court has also ordered a portfolio of shares be transferred to Flinders University.

The money, along with other funds and assets, had been frozen since January 22.