The book follows the adventures of Trot and Cap'n Bill, who previously appeared in two of Baum's fantasy books outside of the Oz series, The Sea Fairies and Sky Island. The two of them are swallowed by the sea in a rowboat and deposited in an underwater cave where they encounter Flipper the Ork, a bird-like Mix And Match Creature. After escaping a long cave system they end up emerging onto an island inhabited by a lone hermit named Pessim. On the island are berries that can change the size of those who eat them, so Trot and Cap'n Bill shrink themselves to enable the Ork to carry them. They then end up in the Land of Mo, as seen in Baum's previous book The Magical Monarch of Mo, where they find Button Bright, and after a brief stay the Ork flies them across the Deadly Desert into Oz.
When they reach Oz, they descend in an isolated micronation known as Jinxland ruled by the corrupt King Krewl, who wants to marry off the rightful Princess Gloria to a decrepit noble named Googly-Goo, though she is in love with the gardener boy Pon. Krewl commissions the evil witch Blinkie to freeze Gloria's heart, and when Cap'n Bill tries to intervene she turns him into a grasshopper. Glinda the Good later gets wind of this situation in her Book of Records, and decides the only one who can remedy the situation is the Scarecrow.
The 1914 film version, His Majesty, The Scarecrow of Oz, actually came out before the book, technically making this a Novelization of sorts, although it differs from the film in many ways. There is some speculation that the novel was also partially recycled from an unfinished third Trot and Cap'n Bill book that wasn't originally going to involve Oz at all; given that no Oz character appears until over halfway through the book, it is an easy speculation to make. However, it is unconfirmed. This was most certainly the case with the next book Rinkitink In Oz, which really was a recycled manuscript that Baum turned into an Oz book.
The Scarecrow of Oz provides examples of:
- Baleful Polymorph: Bill gets turned into a grasshopper by Blinkie, but still has a wooden leg.
- Big Damn Heroes: Flipper comes back with no fewer then 50 of his compatriots to rescue the Scarecrow from being burned by King Krewl.
- Curb-Stomp Battle: When Flipper and all his friends show up from Orkland, the first thing they do is absolutely flatten Krewl, his nasty majordomo and his soliders, summoning a huge tornado.
- Deadpan Snarker: Trot can get really sarcastic to the point of being mean. Case in point, she remarks that Gloria could do better than a lowly gardener like Pon.
- Funetik Aksent: Cap'n Bill certainly talks like an old sailor — minus the swearing, that is.
- Handicapped Badass: Bill's wooden leg might have forced him to retire from the sea, but it doesn't stop him from going on all kinds of magical adventures. It does, however, give him some genuine trouble; with a wooden leg he can't run fast and has problems with uneven ground. The badass part is that he refuses to let this stop him.
- Heart Trauma: The evil witch Blinkie freezes the heart of Princess Gloria of Jinxland to keep her from loving the gardener's boy, Pon. Baum has a very cinematic way of describing the scene, in which an x-ray view of Gloria's heart freezing is seen by the onlookers, which is because the scene is taken from the 1914 film version. When the princess' heart has frozen, she not only acts ice-cold towards everyone but seems incapable of any real emotion.
- I Choose to Stay: Trot and Cap'n Bill are allowed to stay in Oz (with no regard to the fact that Trot has parents, although she seems to have forgotten them completely). Button Bright, now on his second trip to Oz, also decides to stay.
- Incredible Shrinking Man: When Flipper accidentally discovers berries that shrink anything that eats them. After he's restored, the shrinking berries come in very handy when he needs to carry Cap'n Bill and Trot on a particularly long voyage.
- Intergenerational Friendship: Trot with Cap'n Bill, who acts as a father-figure to her.
- Plucky Girl: Very much in the vein of Dorothy, though unlike Betsy Bobbin, Trot was never an Expy and is different enough to avoid becoming a Suspiciously Similar Substitute.
- Noble Savage: Flipper definitely fits into this role, since the Orks disdain technology - they don't even know how to use fire! - and consider themselves higher moral beings then the earth-bound humans. Flipper takes pains to point out that the Orks achieved mastery over their land by being in harmony with it and not driving everything else to extinction.
- Novelization: Based on the 1914 film His Majesty, The Scarecrow of Oz.
- Secondary Character Title: It is quite a while before we encounter the Scarecrow; most of the story details Trot and Cap'n Bill's Canon Immigration into Oz.
- 10-Minute Retirement: Before the Scarecrow, Cap'n Bill and Trot go into Jinxland, Flipper leaves the party to return to his homeland and look up his family. However, he returns with most of his clan in tow - just in time to save the Scarecrow.
- Walking the Earth: Or flying it, in Flipper's case. His wanderlust gets him labeled a Cloudcuckoolander back in Orkland.
- The Watson: Trot occasionally plays this to Cap'n Bill, or when anyone else has backstory they need to convey to the reader.
- Weird Weather: It snows popcorn in Mo, just as in the original book the land appears in.