I know there are many awards for science fiction works in general, such as the Hugo and Nebula. Are there any awards specifically for children's science fiction literature?
The Golden Duck awards "are designed to encourage science fiction literature for children" and have been presented yearly at Worldcon since 1992.
The categories include
Picture Book: Given for books written for very young children.
Eleanor Cameron Award for Middle Grades: Given for books written for grades 2 to 6.
Hal Clement Award for Young Adult: Given for books written for grades 6 to 12.
Special Awards: Given to acknowledge a book, author, illustrator or publisher not fitting in one of the other catagories. This award is created on an as-needed basis.
More recently, the Monica Hughes Award has been honoring Sci-Fi books for adolescents, but only Canadian authors are eligible.
There are quite a few children's SF awards. Most awards for kids' SF are either one in a system of awards or categories within larger awards. The Golden Duck awards are the only ones I can think of specializing in kids' SF, without being part of something bigger.
General awards
SFWA presents the Andre Norton Award for best young adult book at the Nebula award ceremony.
Locus Magazine presents a Locus Award for best YA book.
Golden Duck Awards are given for YA, middle grades, and picture book.
Genre awards
The Horror Writers' Association gives a Bram Stoker Award for superior achievement in work for younger readers.
The Mythopoeic Society presents the Mythopoeic Fantasy Award for Children’s Literature.
Regional awards
Australia's Aurealis Awards have four kids' categories: YA novel, YA short story, children's long fiction/novel, and children's short fiction.
Canada's Sunburst Award gives a YA award.
The Canadian Children’s Book Centre gives several awards for children's lit, including the Monica Hughes Award for Science Fiction and Fantasy.
The Israeli Society for Science Fiction and Fantasy gave a Geffen Award for best YA or children's book, once.
New Zealand's Sir Julius Vogel Awards include one for best YA novel.
And I'm sure there are some I missed, especially for other languages.