A juvenile court judge in Everett found probable cause existed for the murder charge, which automatically transfers the teen to adult court.
The juvenile courtroom was filled Monday morning with the boy's family members, who started crying the moment deputies led the teenager into the room.
Police investigators say the 16-year-old called 911 on Friday afternoon to report a problem at his mother's apartment in the 8200 block of 5th Avenue West - where they found her dead inside.
Detectives later got a search warrant and arrested the teen Saturday afternoon.
In court on Monday he kept his head down, to avoid making eye contact.
Judge Linda C. Krese set his bail at $500,000. If he makes bail she ordered that he must not have any legal violations and that he continue to attend school.
Information provided in court revealed that the teen has been in trouble before and was charged last year with assault for an incident at school.
The prosecutor's office has 72 hours to charge the teen as an adult, and at that time he would make his first appearance in Superior Court, later this week.