Benjamin Mee is recently widowed, and his 14-year-old son, Dylan, is expelled from school. Benjamin decides to begin again in new surroundings, wanting to get away from the sad reminders of his deceased wife. He finally buys a large house with a zoo in the backyard; at first reluctant to take on the zoo with its animals, he decides to give it a try. Although his young daughter, 7-year-old Rosie is happy with the animals, Dylan is unhappy and retreats into his art work. Benjamin meets the staff of the zoo, headed by the attractive Kelly Foster. They must meet stringent requirements in order to open in the summer, and proceed to work to upgrade the zoo’s facilities. Meanwhile, Dylan and 13-year-old Lily Miska begin a friendship, although Dylan is shy and uneasy initially. While Benjamin is working on reconstructing the zoo, Dylan isn’t so happy about moving and hides in the shed and starts working on his drawings, although Lily, (who now has a crush on Dylan) gives an unexpected visit and gives him a sandwich along with a suggestion for his drawings. Lily promises Dylan that she will visit him and give him a sandwich every day at four-fifteen. After she leaves, Dylan unwraps the wrapper for the sandwich, finding a note with a welcoming hello from Lily.
The zoo runs into trouble when Benjamin’s bank account starts to run out of money. The morale of the workers starts to dip, as they think that Benjamin will sell the property away like the previous owner. At the same time, Lily becomes upset with Dylan after he was happy to hear the rumor that the family might be shifting away from the zoo. Benjamin miraculously discovered that his late wife had an investment account, with instructions for Benjamin to use the money wisely while listening to his heart and ignoring his older brother. This discovery lifted the spirits of the zoo’s workers. When Dylan is left alone a few days later, by heartbroken Lily who decides not to see him any more after what happened earlier, and results breaking the promise she made. The same night, Dylan overhears Benjamin saying the reasons why he was so strict with Dylan. Heartbroken, he starts quarreling with his father. However, the pair manages to reconcile the next morning. When Dylan admits he misses Lily, Benjamin gives his son advice on reconciling with her, saying that he just needed “20 seconds of insane courage”. Dylan’s art work was also chosen as the zoo’s official logo.
One week before the opening day, Walter Ferris inspects the zoo and finally gives it his approval. At the day before the zoo’s opening, Lily, unsure if Dylan likes her back, bravely puts up a neon sign with the words “If you love me, let me know.” Dylan happens to see it while he was walking home in the rain, and finding it his only chance to confess to Lily, he goes to Lily’s bedroom window to reconcile with Lily and to confess that he loves her. Lily hesitates at first, but forgives Dylan and they both hug. Although the town experienced the worst rainstorm in a hundred years that threatens to wash out the opening of the zoo, the day turns out to be sunny. They later realized that a tree that has fallen had blocked the access road, leaving many visitors unsure if the zoo is opened. Undaunted by this setback, Benjamin and the staff help the visitors over the tree. This zoo proves to be a hit amongst the town citizens. At the end, Benjamin shows the kids the place where he met their mother, telling them that was the point in both their lives where the kids became a possibility. He tells and shows them what he said and did. They all imagine their mother siting there like when Benjamin first met her. After Benjamin says to her, “Why would an amazing woman like you talk to someone like me?”, she replies, “Why not?”.