The mother, who chose to be identified only as Wendy, said she rushed her daughter to hospital after seeing her put the condom in her mouth and is now worried the girl may have contracted an STD.
She added it could take two months to find out from blood tests if her daughter has an infection.
“I don't know how it happened but when my husband next looks at her, she's sucking on a black condom,” Wendy said.
“I ran into the bathrooms, washed her mouth and hands and came out and gave her a drink. We were terrified,” she added.
"I am really angry and sickened... I haven’t slept. I have been feeling overwhelmingly guilty for taking her there in the first place.”
She said the condom looked used, but she could not see any packaging for it.
The parents went to speak to a local doctor, who told them to go back to the restaurant to get the condom for testing.
Wendy said when she asked McDonald’s staff, they refused to give her the condom.
"What if there is an STD there and my daughter is going to get it? We have to wait two months to do a blood test on her," she said.
A McDonald's spokesperson said the Warnbro restaurant was investigating the incident and they believed an employee did take the condom to the hospital.
“We are very sorry that the incident occurred, and take situations like this seriously," they told WAtoday.
"Cleanliness and safety are our top priorities and we ensure the shift manager on duty conducts what we refer to as a travel path every 30 minutes.
"The travel path sees the shift manager walk through and check all areas of the restaurant.”