Officers were called to the Cornton area of the city at about 21:45 on Friday after reports that two children had become unwell.
The pair were both taken to hospital where they are being treated for non-life threatening injuries.
A man has been arrested and charged over the incident.
Police Scotland has now issued a drugs warning as officers believe they suffered an "adverse reaction".
Chief Inspector Damian Armstrong said: "This incident is very concerning and highlights the dangers of taking illegal drugs.
"I would urge members of the public to be aware of the dangers of illegal drug use and advise anyone who has taken drugs and feels unwell to seek urgent medical advice.
"Additionally I would ask anyone with information that can assist us with our ongoing investigation to please get in touch."
A 12-year-old boy and 14-year-old girl in Stirling have been taken to hospital after taking an "illicit substance", police have said.