Recently widowed Benjamin (Ben) Mee (Matt Damon), still grieving his loss and dealing with school behavior issues and the expulsion of his 14-year-old son Dylan (Colin Ford), decides to get a fresh start by buying a new house. After touring many houses with his daughter Rosie (Maggie Elizabeth Jones) and his realtor, Mr. Stevens (JB Smoove), and finding none to his liking, his daughter finds a paper with what seems like his perfect house. They drive up to a beautiful old large house and Ben inspects the property, telling his realtor it's the perfect home. As he tries to explain that the situation is "complicated", they hear a lion roar outside. The realtor explains that the house comes with a zoo at the back and, if they want the house, they have to buy the zoo which closed to the public several years before.
Although reluctant to take on a zoo and all of its animals, he decides to give it a try when he sees how happy Rosie is playing with the peacocks. Dylan, however, hates the idea of moving away from his friends, retreating into his artwork which has grown more macabre since the death of his mother. Ben's brother Duncan (Thomas Haden Church) tries to dissuade him from purchasing the property, but Ben buys it anyway. The zoo staff, led by the 28-year old head keeper Kelly Foster (Scarlett Johansson), help Ben to start renovating the zoo with the intent to reopen it to the public. When Kelly confronts Ben about why he bought a zoo, knowing nothing about how to run one, Ben thinks about it and responds "Why not?". Dylan befriends Kelly's 13-year old homeschooled cousin Lily Miska (Elle Fanning) who works at the zoo and has a huge crush on him, to which he is completely oblivious.
A strict USDA inspector, Walt Ferris (John Michael Higgins), shows up for a surprise inspection and makes a large list of repairs that would cost around $100,000. Ben runs into financial trouble with the expenses of running the zoo and does not have the money for the repairs. Rhonda Blair (Carla Gallo) the zoo worker that handles the accounting, gossips to the other workers that Ben is out of money and that he will probably sell the zoo; after which the workers' morale sinks, fearing the property will be sold to a buyer that will close it down. When Lily tells Dylan that she heard his family might be leaving, he is overjoyed, which hurts her feelings. Ben discovers that his wife bequeathed him an investment account, with instructions to use the money wisely while listening to his heart. Duncan advises him to walk away and start over with the money, but Ben decides to use the money to repair the zoo. While this lifts the zoo workers' morale, Dylan is unhappy about having to stay; he confronts his father, and a heated argument ensues. They reconcile the next morning, and Dylan admits he misses Lily. Ben gives his son advice using his favorite principle, that you only need 20 seconds of courage to achieve great things in order to reconcile with Lily. Ben realizes that instead of trying to start over by forgetting his wife, he should accept that she will always be a part of him.
Prior to the grand opening of the zoo, the facility passes a very stringent inspection from Ferris, who begrudgingly wishes them good luck. Dylan, following his father's advice, confesses to Lily that he loves her and she forgives him. The evening prior to the zoo's grand opening the worst rainstorm in 100 years is predicted to wash it out and, although the weather clears in time, they are disappointed the next morning when no visitors arrive, though they soon discover that a fallen tree has blocked the access road. Scrambling over the tree, they discovers a huge crowd of waiting visitors, who climb over the tree with the zoo staff's help, and pour into the zoo. So many people come to visit that they run out of tickets forcing Ben and Kelly to enter a shed to look for them, ending up face to face. Kelly admits to Ben that she has a crush on him but she "can't get a handle on it". She kisses him, telling him maybe they can do that again on New Year's eve - Ben replies by kissing her, and telling her that he is looking forward to it.
Ben takes his children to the restaurant where he met their mother, explaining that it was the point where they became a "possibility". He takes them through that day's encounter, where Ben worked up the nerve to talk to his future wife with "20 seconds of courage", and walks up to the table she was at, visualizes her sitting there, then asks her why such an amazing woman would talk to someone like him. His wife responds "Why not?", echoing the reason Benjamin bought the zoo in the first place.
- Matt Damon as Benjamin Mee
- Thomas Haden Church as Duncan Mee
- Colin Ford as Dylan Mee
- Maggie Elizabeth Jones as Rosie Mee
- Scarlett Johansson as Kelly Foster
- Desi Lydic as Shea
- Patrick Fugit as Robin Jones
- Elle Fanning as Lily
- Stephanie Szostak as Katherine Mee
- John Michael Higgins as Walter Ferris
- Angus MacFadyen as Peter MacCready
- Carla Gallo as Rhonda
- Peter Riegert as Delbert McGinty
- J.B. Smoove as Zoo Seller