One charge is in connection with a sibling at the nursery in Kalmar, southern Sweden, where he carried out his assaults. The other charge concerns an incident that occurred in the past and is not connected to the day-care.
The authorities have classified both new charges as sexual molestation.
On Wednesday the man was charged for 13 sex crimes against children at the nursery. He is suspected of both rape and sharing images of the children online.
Following his indictment another child at the nursery came forward which led to his charge for assaulting a sibling of one of the children at the day-care.
Police do not presently have all the details regarding the earlier assault charge, which did not take place at the day-care.
"We are looking at whether he was at the age of criminal responsibility when the abuse must have happened,"Lina Isaksson Funke, Police public relations officer, told the TT news agency.
The man was indicted on 26 points on charges including aggravated child rape, multiple sexual assault charges and possession and distribution of child pornography.
Court prosecutor Linda Caneus said he began his internship at the nursery on January 27th and worked there until April 3rd, adding that he carried out assaults on both his first and last days working there.
The majority of the victims were between two and six years of age, and the youngest had not yet turned two.
He has already confessed to several of the molestations. A preliminary investigation has indicated that the man may suffer a serious psychiatric disturbance.
His trial is due to begin on Wednesday.