The employee has since been fired from the school, which is a school for students with special needs.
The mother of the student spoke out on Thursday and said what Matthew Nelson, 32, did could have killed her son.
"At first I was in shock thinking how can someone take my son's medicine. Then the fact they replaced it was mind boggling. Who would do that to a child," she said.
The Encinitas mother asked not have her identity revealed.
Nelson was the behavior analyst at the country school in San Marcos.
According to a Sheriff's report, he was caught on surveillance camera stealing Ritalin tablets on March 4th, from the school's medicine cabinet. He allegedly replaced them with Claritin Allergy medication, a drug that according to student's mother, her son has had serious reactions to.
A staff member noticed the pills had a different tint after the student had already received one dose of medication.
"If they would have not have caught it in first dose, but the second or third dose, because he takes three doses a day at school, we would have been in the hospital. He could have had a seizure. he could have been dead," she said.
The mother of the student is upset with the way the school handled the situation.
"I was the one that called the police. I feel like they were trying to sweep things under the rug. I really do," she said.
The director of the school confirmed Nelson is no longer an employee and in a statement said, "The matter is in the hands of the authorities with whom we we have been and remain in full cooperation with."
Nelson now faces charges of felony burglary and misdemeanor theft, according to the report.
Nelson confessed to switching the medication and said he is an addict. He has checked himself into rehab.
He spoke to CBS News 8 and said he pleaded guilty. He is now awaiting sentencing.
He said he wants the students and families to know he is terribly sorry.
The student's mother has contacted the Department of Education in regards to the incident.
Nelson will be sentenced later in May. He faces three years behind bars, but according to the district attorney's office, a sentence has already been agreed upon by both parties.