Kotb was born in Norman, Oklahoma, but grew up in Morgantown, West Virginia. Both of Kotb's parents are from Egypt. Along with her parents, she has also lived in Nigeria. In Arabic, the name "Hoda" means "guidance", and is very popular among Arab women. The surname "Kotb" means "the pole", and is a common surname among Egyptians. The name is usually pronounced . For a period during her career, she spelled her surname Kotbe to aid in pronunciation; she now uses the original form, Kotb.
Kotb graduated from Fort Hunt High School in the Fairfax County section of Alexandria, Virginia in 1982, where she was also elected Homecoming Queen. In 1986, she graduated from Virginia Tech with a Bachelor of Arts in broadcast journalism. She is a member of Delta Delta Delta Sorority.
In March 2007, Kotb underwent a mastectomy and reconstructive surgery for breast cancer, and has since become an advocate for breast cancer awareness. Kotb allowed Today Show cameras to follow her throughout her cancer ordeal and, after she was announced cancer-free, her story was documented on the show.
She was the keynote speaker at her alma mater for the 2008 Virginia Tech graduation, where she played "Enter Sandman" over her iPod.