The two grants come from the federal Affordable Care Act, a comprehensive health care reform law signed by President Obama in 2010, officials said.
A larger grant of $2,413,505 will be used to renovate the hospital's primary care clinic, which serves more than 30,000 patients each year.
The grant will allow renovations that will nearly double the number of exam rooms, and provide more space for pediatric sub-specialists to see patients within the clinic.
Bringing in specialists will assist the large population of patients covered by MediCal government insurance who travel to the Oakland hospital and have challenges finding specialists who accept MediCal insurance, according to hospital officials.
A second grant of $500,000 will be used for renovations to the hospital's teen clinic and its Center for the Vulnerable Child.
The teen clinic, which provides comprehensive medical and mental health services for teenagers, receives around 1,300 patients each year, hospital officials said.
The Center for the Vulnerable Child is the only clinic in the country dedicated to providing care for homeless children and children in foster care, hospital officials said.
About 3,000 children receive medical care, psychotherapy and social services through the center, and its expansion will allow the hospital to serve even more children and provide more services.
"The Affordable Care Act grants are a tremendous achievement for Children's Hospital and Research Center Oakland. This funding enables us to continue our 100-year-old mission to care for our community's children in need," hospital President and CEO Bretram Lubin said in a statement.