Zlata's Diary is a collection of reprinted entries from the journal of Zlata Filipovic, a child who wrote during the Bosnian War from 1991 to 1993. They offer an innocent child's first-hand perspective on the horrors of war.

Initial entries (before war) present a normal pre-teen girl who enjoys hanging out with her friends, taking piano lessons, vacationing, and doing well in school.

The first hint of war comes when Zlata's father is recruited into the police reserves, and violence breaks out in the nearby region of Dubrovnik. The family worries about a family friend, Srdjan, living in that region. Zlata does not understand the reasons for this conflict, but is confident that war coming to her own country of Bosnia-Herzegovina would be "impossible."

But in March 1992, violence indeed breaks out in her city of Sarajevo as Serbian nationalists attack. Gunfire from the hills and shelling will be a near-constant reality from this point forward. Zlata's family must often hide in a neighbor's cellar to be protected from the shrapnel and bullets. The nationalists conquer one part of the town, and many are killed and wounded.

On May 2, the local post office is torched and the president of the country is kidnapped in the worst day of fighting yet. Many flee, including most of Zlata's friends. Zlata's uncle Braco is hurt in an accident and must spend several months in bed. Water and electricity go in and out, and food becomes harder to come by. The family must usually cook with an old wood-burning stove. The United Nations gets involved during this period, and the family comes to rely on care packages for food and other essentials.

The community copes as best it can. Birthdays are celebrated with large gatherings and whatever food can be found, and a temporary summer school is established which Zlata attends. It is through a friend and her summer school teacher, Irena, that Zlata gets the opportunity to have her diary entries published by the humanitarian organization UNICEF.

Through her work, Zlata's mother has a chance to escape the country with Zlata, but bureaucracy spoils the opportunity. Meanwhile, many of Zlata's friends or friends of the family, including a young man named Nedo that Zlata grows very fond of, escape on various convoys. Fortunately, Zlata is able to spend a lot of time with one of her best friends, Mirna.

On July 17, 1993, Zlata attends a promotion for the book made from her diary. She becomes an international celebrity, and thereafter is continually interviewed by journalists from around the world.

In mid-September 1993, there is some talk of a conditional peace accord, but by mid-October gunfire is still erupting from the hills surrounding the city. Zlata's last entry asks a simple question of the war: why?