The protagonist is Prosper, a twelve-year-old boy who runs away from his aunt and uncle when they try to adopt his brother but not him. Prosper is intelligent and cunning, and fiercely protective of his younger brother Bo; he views his aunt and uncle as predatory and thinks that they only want to take Bo from him and keep him out of their family and Bo's life.
Prosper... couldn't help looking around as if he expected his aunt to be lurking in the crowd, just waiting for her chance to grab Bo.
While there is no clearly defined central antagonist (constantly working against the protagonist), a good candidate is Ernesto Barbarossa, an antiques dealer and fence for stolen items. While he initially seems to be on the side of the orphans, it turns out that he only wants to swindle them out of the valuable items that they steal, and he receives his comeuppance when he is turned into a child.
...Ernesto Barbarossa. A fat man with a red beard, Barbarossa had an antiques shop where he sold cheap trash... he also did secret deals with more valuable, and usually stolen, items.
(Funke, The Thief Lord, Google Books)
Other possibilities for antagonist are Prosper's aunt and uncle, who don't care about Prosper's future but only want a small child without hassle, or Victor Getz, a private detective who initially searches for the boys but then becomes an ally.