A man named Timothy Templeton (Tobey Maguire) tells a story through his imaginative point of view as his 7-year-old self (Miles Bakshi) who lives his days having fun with his parents, Ted (Jimmy Kimmel) and Janice (Lisa Kudrow), and wishes it to be just the three of them forever. While tucking Tim in bed one night his parents ask if he wanted a baby brother; Tim declines the offer, saying that he is enough. After he goes to sleep, we see that Janice is pregnant.
While sleeping Tim begins to wonder where babies come from. One day, Tim is surprised when a business suit-wearing infant shows up in a taxi at his house, and Ted and Janice proudly call him Tim’s little brother. Tim is envious of the attention the baby is receiving, not to mention suspicious when the infant acts odd around him, but his parents, being blind to the baby’s eccentric behavior, try to convince him that they will grow to love each other.
Soon, Tim learns that the baby can talk like an adult (Alec Baldwin) and he introduces himself as ”The Boss”. Seeing an opportunity to be rid of him, Tim decides to record a conversation between him and other toddlers who are over at Tim’s house for a meeting (under the guise of a playdate by the parents) to do something about how puppies are receiving more love than babies. The Boss Baby and the other infants catch Tim with the recording and after a chase scene throughout the backyard and the house, the tape is terminated after The Boss Baby threatens to tear up Tim’s favorite stuffed animal, Lam-Lam. With no evidence to support him, Tim is subsequently grounded by his parents for his actions during the chase between him and the infants, much to Tim and even Boss Baby’s dismay.
The Boss Baby comes to Tim and apologises to him and has him suck on a pacifier that transports them to Baby Corp, a place where infants with adult-like minds work to preserve infant love everywhere. They are virtual, so they cannot be seen or heard. The Boss Baby explains to Tim that he was sent on a mission to see why puppies are getting more love than infants. He has infiltrated Tim’s residence because his parents work for Puppy Co., which is unleashing a new puppy on the day that employees take their children to work. The Boss Baby also explains that he stays intelligent by drinking a ”Secret Baby Formula” which enables a baby to act like an adult. However, if a baby does not drink it after a period of time, he or she reverts to a regular baby. He hopes to receive a promotion after dealing with Puppy Co.’s new puppy, but when they overhear Boss Baby’s boss threaten to fire him for not bringing in information, thereby stranding him at the Templetons, he and Tim agree to work together to keep that from happening.
After appearing to have patched things up, Tim’s parents lift the grounding and take them to Puppy Co. for ”take your child to work day”. While there, they slip away and find what they think is the plans for a ”Forever Puppy”, but it turns out to be a trap set by founder Francis E. Francis (Steve Buscemi). They discover that Francis used to be the head of Baby Corp. and Boss Baby’s idol, but was forced out when it was discovered that his lactose intolerance kept the secret formula from working properly. Vowing revenge, Francis founded Puppy Corp. and intends to have the Forever Puppies overshadow babies by stealing Boss Baby’s serum bottle and infecting the puppies with it. Tim’s parents go with Francis to Las Vegas, and Francis has his brother Eugene (Conrad Vernon) pose as Tim and Boss Baby’s babysitter to keep them from interfering.
Without a steady flow of serum to keep his intelligence in check, Boss Baby begins reverting back to being a normal baby. Despite this, he and Tim manage to evade the ”babysitter” long enough to get to the airport, but are too late to intercept Tim’s parents. Upset, Tim blames Boss Baby for using his family for his own ulterior motives, for which Boss Baby, after some hesitance, apologizes. After sneaking on a plane for Elvis impersonators (James McGrath and James Izzo) bound for Vegas, they stall Francis’ presentation when Eugene (disguised as another Elvis impersonator) unwittingly gives away their plan, which they begin to have a good time together with Tim’s imagination in the plane.
Furious at their interference, Francis proceeds to lock Tim’s parents up so he can burn them with exhaust from a rocket used to launch the Forever Puppies. Tim and Boss Baby fight with him, and then push him off the ledge, making Francis plummet into the formula. Boss Baby opens the rocket to let the dogs out, so they can save Tim’s parents. After he successfully does that, he returns to baby state while still on the rocket, but Tim sings to him with a family song to show his appreciation, causing him to jump off of the rocket before it launches. Francis, having reverted back to baby form, attempts to attack them again, but Eugene interferes, stating he’ll ”raise him right this time” now that he’s a baby again.
Boss Baby gets promoted, leaves in a taxi, and Tim goes back to being an only child. But Tim and Boss Baby, having grown closer, start to miss each other (which they discover that love don’t change places but multiples instant). Boss Baby, fed up, decides to be part of the Templeton family permanently. He returns to the Templeton family as a regular baby named Theodore Lindsey, as the whole story turned out to be in Tim’s imagination, and Ted and Janice have just brought him home from the hospital.
Back at the present, Tim who finished the story is now an adult and now the father of an older daughter (which he told the story to her) and an infant daughter who was just born and acts exactly like Theodore did when he was Boss Baby (or at least according to Tim’s older daughter vision of things, suggesting that her father’ story influenced her or at least she had a similar imagination or more probably: older Tim’s story is in fact real.)