Kids will be provided with food, medical care and a place to sleep and shower.
An outdoor recreational area will also be created on the site.
A date for the first arrivals is still being finalized.
San Diego officials say they were requested to provide the center by federal Health and Human Services Secretary Xavier Becerra, the former California state attorney general, and federal funding will be provided.
San Diego Mayor Todd Gloria and county Board of Supervisors' Chair Nathan Fletcher released a statement saying when they got the request "we knew it was the right thing to do."
"We are working closely with our federal partners to finalize the details for preparing to receive these young people and provide them with care, compassion and a safe space to transition while they are reunited with families or sponsors."
San Diego officials expect the site to be used for that purpose for about three months, with each child expected to stay there an average of 30 to 35 days.