Eduardo Cristobal, 18, was arrested Wednesday in the incident that occurred while the boys, ages 12 and 13, were trick-or-treating in east San Jose.
Police said the boys were confronted by a group that mistook them for members of a rival gang.
The 12-year-old was in critical condition after being shot. His friend was treated and released for stab wounds.
Police said they were not gang members and were not wearing anything on Halloween to indicate they were in a rival gang. No further details were provided.
The other suspects were identified by prosecutors as Erik Diaz, 16, Diego Gutierrez, 16, and Hugo Torres, 15.
The four suspects were being held in Santa Clara County Jail for investigation of attempted murder. They were scheduled to be arraigned next week and do not yet have lawyers.
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