It is also the same church, in Davington, near Faversham, in Kent, where the funeral was held for her mother Paula Yates in 2000.
The 25-year-old television presenter, model and socialite, died suddenly two weeks ago at her home.
The cause of her death is not yet known as a post-mortem test was inconclusive.
The results of toxicology tests are expected in the coming weeks, after which, an inquest is expected to be opened.
Her body was found at the home she shared with her husband, musician Thomas Cohen and their sons, Astala, 23 months, and 11-month-old Phaedra, in Wrotham, Kent.
Police have said the death is being treated as a "non-suspicious, unexplained sudden death".
Her funeral will be held at St Mary Magdalene and St Lawrence Church Geldof married Thomas Cohen, lead singer of the band SCUM, in 2012The Geldof family said the service would be private.
Sir Bob, the former Boomtown Rats singer, has described his daughter as the "wildest, funniest, cleverest, wittiest and the most bonkers of all of us".
The church is also where Sir Bob and television presenter Yates married in 1986. She died in 2000 from a heroin overdose.