Little Men follows the life of Jo Bhaer and the students who live and learn at Plumfield School that she runs with her husband, Professor Bhaer. Jo inherited the estate from her Aunt March. The mischievous children, whom she loves and cares for as her own, learn valuable lessons as they grow to adulthood. While the story focuses mainly on Jo, her husband and the pupils, characters from "Little Women" continue to appear. Meg is now married to John Brooke, with twins at the school; Amy is married to Laurie, and occasionally visits with her small daughter, though Laurie makes more regular appearances.
The story begins with the arrival of Nathaniel "Nat" Blake, a shy young orphan with a talent for playing the violin and a penchant for telling fibs. Through his eyes we are introduced to the majority of the characters, from the Bhaers' children to other classmates. We follow Nat's life from April through Thanksgiving, meeting new students and playing games and having adventures throughout.
Nat is the twelfth boy to arrive at the school, though the twelve include Jo's own sons Rob and Teddy, who are significantly younger than the others and do not attend formal lessons (Dick and Adolphus, known as Dolly, are eight years old; Professor Bhaer's nephew Franz is sixteen). Franz's younger brother Emil is also at the school, and so are Meg's twins, Daisy and Demi.
Nat realises immediately that the school is not run on conventional lines, as he arrives during the Saturday night pillow-fight, which Mrs Bhaer not only permits but even joins. All the children have their own gardens and their own pets, and spend time on these as well as in regular lessons. Discipline is also unusual; Nat is ordered to strike Professor Bhaer's hand with the cane, rather than being caned himself, as a punishment for telling lies.
There are two further new arrivals shortly afterwards, both of which significantly alter the character of the school. The Bhaers are concerned that Daisy, the only girl (except for the occasional visits from Laurie and Amy's tiny daughter Bess) is regularly left out by the boys. Jo and Laurie set up a miniature kitchen for her, but this is time-consuming for Jo and does not provide her with companionship. They therefore decide to make the school more co-educational and to invite Annie (Nan) to join them. Nan is a tomboy after Jo's own heart and becomes friends equally, though very differently, with prim Daisy Brooke and chaotic Tommy Bangs.
The other new student is introduced by Nat himself, who believes that the school will manage to accept and reform his rough-mannered friend. Dan, however, decides the other boys are "molly-coddles" and leads them in experiments with fighting, drinking, smoking, swearing and playing cards, which results in his being temporarily removed from the school. He returns eventually with an injured foot, and redeems himself by standing up for Nat when Nat is falsely accused of theft by the other boys. He also becomes curator of the school's natural history museum.
Each student has his or her own struggles: Nat lies; Demi, although adored by his mother and sister, is so naïve that he finds it hard to live in the real world, but swears that he will be like 'papa' after John Brooke (Meg's husband) dies; Emil has a bad temper; Dan is rebellious and rude; Tommy is careless (and once sets the house afire); Annie alias Nan is too tomboyish; Daisy is too prim and even weak-willed etc. They all learn to cope with their faults as they grow into young men and women.