Since no one has ever bothered to explain the importance of learning to Milo, he regards school as the biggest waste of time in his life. Juster intended that the book speak to the importance of learning to love learning. Teaching methods that might bore children, by memorization for example, are mocked in the book, as in the case of the Spelling Bee. Like the Bee, the Humbug's insult to his fellow insect goes over Milo's head, but possibly not the reader's: "A slavish concern for the composition of words is the sign of a bankrupt intellect." According to Mary Liston in her journal article on law in fantasy realms, "The Phantom Tollbooth concerns the difference between education and wisdom and what processes are conducive to synthesizing both, so as to encourage an attitude of engagement, alertness, and responsibility within an increasingly autonomous individual."
"BOSH!" replied the Humbug. "We're an old and noble family, honorable to the core—Insecticus humbugium, if I may use the Latin. Why, we fought in the crusades with Richard the Lion Heart, crossed the Atlantic with Columbus, blazed trails with the pioneers, and today many members of the family hold important government positions throughout the world. History is full of Humbugs."The Phantom Tollbooth (in Dictionopolis) 
Another theme is the need for common sense to back up rules. Milo journeys through a land where, without Rhyme or Reason, the art of governance has been lost, leading to bizarre results. Milo repeatedly meets characters to whom words are more important than their meaning. The Whether Man, for all his talk, is unable to provide Milo with the information or guidance the boy wants, while Officer Shrift's investigation of the overturning of the Word Market contains the forms of law, without justice. The denizens around Digitopolis are little better; the twelve-faced Dodecahedron, named for what he is, turns the logic of his naming on its head when he asks if everyone with one face is called Milo. The attitudes now displayed by the adherents of both brothers are summed up by the Dodecahedron, "as long as the answer is right, who cares if the question is wrong?"
As Milo struggles with words and begins the process of making himself their master, he also has difficulty with numbers, especially when he speaks with .58 of a child, who with parents and two siblings (whom Milo does not meet) makes up an average family. Milo has had difficulties in school with mathematics and problem solving; his reaction to this encounter is to protest that averages are not real. The partial child enlightens Milo that there is beauty in math beyond the tedium of learning an endless set of rules, "one of the nicest things about mathematics, or anything else you might care to learn, is that many of the things which can never be, often are". Late in the book, Princess Reason counsels Milo, who has much learning ahead of him, not to be discouraged by its complexity, "You must never feel badly about making mistakes ... as long as you take the trouble to learn from them. For you often learn more by being wrong for the right reasons than you do by being right for the wrong reasons". An index card in the Juster papers sets forth the germ of the princess' "memorable" counsel to Milo, "Quite often the road to Rhyme + Reason is through the right mistakes."
Although Milo is bored with learning, that does not mean he knew nothing before his journey. He exhibits characteristics of a well-schooled child of his time; his speech is polite and peppered with "please" and "thank you", and when he unexpectedly encounters the partial child, he requests pardon for staring. He can count to a thousand, though his tact in bringing up the subject in the presence of the numbers-hating King Azaz is not the best. Mindful of his mother's admonition to eat lightly when a guest, he initially orders a light meal at the banquet, only to find the waiters bringing in insubstantial light beams. Not realizing he will be asked to eat his words, he then makes a plausible start at a speech before being interrupted by the king. The Phantom Tollbooth displays Milo's growth; Leonard S. Marcus in his notes to its annotated edition writes that the boy learns to think in the abstract, pledging after his unintentional jump to Conclusions that he will not make up his mind again without a good reason. Milo does not accept the word of the demon of insincerity that he is a threat and is rewarded by learning he is not. Just for a moment, Milo is able to float in the air beside Alec Bings and see things from the perspective he will have as an adult, allowing the young reader to contemplate what it will be like to do the same. According to Liston, Milo "transforms himself from an unthinking and compliant Lethargarian to a young adult with greater consciousness, a firmer sense of self, and a newly found set of responsibilities".
Even though the day is won by Milo and his fellow questers, it is a great but not a permanent victory, as he hears the kingly brothers begin to argue again as he departs. Juster has written that it was his intent to get Milo out of there as quickly as possible, and that "the fight would have to be won again and again".
Milo's trip through the lands beyond the tollbooth teaches the previously bored child to appreciate both journey and destination. This is a lesson that had been unlearned by the citizens of Wisdom, as exemplified by the described fate of the twin cities of Reality and Illusions. Although the city of Illusions never actually existed, Reality was lost as its residents concentrated on getting to their destination as quickly as possible, and, unappreciated, the city withered away, unnoticed by the busy people who still hasten along its former streets. Milo meets his trials by defining himself as different from the kingdom's inhabitants, who either demand or accept conformity, as enforced by the kingdom's laws, which discourage (and even outlaw) thought. Milo cannot accept such laws, beginning when, in the Doldrums, he thinks, thus violating a local ordinance and separating himself from the thoughtless inhabitants. Liston opined that because the Kingdom of Wisdom's "laws require the impossible, they contradict what it means to be fully human".