In the deep jungles of Darkest Peru, a British geographer discovers a previously unknown species of bear. He is about to shoot it to take back a specimen to the United Kingdom when a second bear playfully takes his gun away and saves his life by removing a deadly scorpion from his jacket. He learns that the bears are intelligent and can learn English, and that they have a deep appetite for marmalade, and names them Lucy (after his mother) and Pastuzo (after a boxer). As he departs, he throws his hat to Pastuzo and tells the bears that they are always welcome if they wish to go to London.
Forty years later, the two bears are living in harmony with their orphaned nephew, until an earthquake destroys their home, forcing them to seek shelter underground. Uncle Pastuzo fails to reach the shelter in time and is killed by a falling tree; his nephew finds his hat the next morning. Aunt Lucy encourages her nephew to go and find solace in London by stowing away on a cargo ship, while she moves into the Home for Retired Bears.
The young bear arrives in London and eventually reaches Paddington Station, where he meets the Brown family, who take him home temporarily and name him after the station they found him in. Henry Brown, the father and a devoted risk analyst, does not believe Paddington's story, and is adamant that Paddington stay only one night while they find a place for him to live permanently, but his wife Mary, an illustrator, and their two children, Jonathan and Judy, find him endearing, as does Mrs. Bird, the housekeeper.
Paddington thinks he can find a home with the explorer who found Aunt Lucy and Uncle Pastuzo, but does not know his name. Since there seems to be no word of his expedition anywhere on the Internet, Mary takes Paddington to Samuel Gruber, an antique shop owner who discovers that the hat bears the stamp of the Geographers' Guild, but the Guild has no record of an expedition to Peru. With the help of Henry, Paddington infiltrates the Guild's archive and discovers an expedition to Peru was undertaken by the explorer, whose name is Montgomery Clyde (although the Guild erased their record of the expedition).
Meanwhile, the hateful museum taxidermist Millicent Clyde captures, kills, and stuffs exotic animals to house in the Natural History Museum. When she becomes aware of Paddington, she immediately sets out to hunt him down. The Brown family departs for the day, leaving Paddington home alone. Scheming with the Browns' nosy next-door neighbour, Mr. Curry, Millicent sneaks in and attempts to capture Paddington; he manages to defend himself, but inadvertently starts a fire in the kitchen in the process. Disbelieving Paddington's statement of Millicent's capture attempt, Henry states that they must take him to the authorities as soon as possible and Mary reluctantly agrees.
Feeling unwanted, Paddington leaves and attempts to track down Montgomery Clyde himself, using the phone book to track the addresses of every "M. Clyde" in London. He eventually finds Millicent's house, and learns that Montgomery Clyde, who was Millicent's father, died a long time ago. Millicent resents her father for losing his membership of the Guild after he refused to bring a Peruvian bear specimen home, even though it would have made his family wealthy, and subsequently opened a petting zoo. Millicent is determined to succeed where her father failed, by stuffing Paddington so she can become rich and famous herself. She tranquilizes Paddington and prepares to stuff him, but when Mr. Curry discovers her true intentions, he informs the Brown family and they rush to save Paddington. They rescue him, and after reaching the roof, Paddington subdues Millicent by throwing a marmalade sandwich (which he keeps in his hat for emergencies) at her. This attracts a huge flock of pigeons, distracting her, before Mrs. Bird opens a roof hatch, pushing her off the roof and trapping her on a flagpole.
In the aftermath, the Browns allow Paddington to move in with their family. Millicent is arrested and subsequently sentenced to community service at the petting zoo her father opened. Paddington writes to Aunt Lucy, saying he is happy and has finally found a home. He is later seen enjoying a snowball fight with the Browns, and throws one at the camera before the film ends.
Ben Whishaw as the voice of Paddington Bear
Hugh Bonneville as Henry Brown
Sally Hawkins as Mary Brown
Madeleine Harris as Judy Brown
Samuel Joslin as Jonathan Brown
Julie Walters as Mrs. Bird
Nicole Kidman as Millicent Clyde
Lottie Steer as Young Millicent
Peter Capaldi as Mr. Curry
Jim Broadbent as Samuel Gruber
Imelda Staunton as the voice of Aunt Lucy
Michael Gambon as the voice of Uncle Pastuzo
Tim Downie as Montgomery Clyde
Simon Farnaby as Barry
Matt Lucas as Joe
Matt King as Andre the Thief
Madeleine Worrall as Agatha Clyde
Geoffrey Palmer as the head geographer
Michael Bond as the kindly gentleman
Based on the stories of the character Paddington Bear created by Michael Bond