Israeli authorities failed to inform parents of their children's arrest or whereabouts, the New York-based watchdog added, drawing on accounts of several children detained during intense unrest in east Jerusalem and the West Bank late last year.
HRW's Middle East director Sarah Leah Whitson urged the United States to pressure its Israeli ally to end what it said were long-standing "abusive practices".
The rights group issued the accusations as US Defence Secretary Ashton Carter began a visit to Israel.
"Forces have choked children, thrown stun grenades at them, beaten them in custody, threatened and interrogated them without the presence of parents or lawyers, and failed to let their parents know their whereabouts."
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Israel's army, when contacted by AFP, had no immediate comment on the report.
HRW said the military and justice ministry responded to its accusations and maintained that "security officials had adhered to the law in all cases, including by informing the children of their rights".
Rashid was accused of throwing stones during the months of unrest that rocked Jerusalem before and after a deadly July-August war in the Gaza Strip.
The Jerusalem riots, where security forces clashed with stone-throwing Palestinians, were accompanied by a spate of killings of both Jews and Arabs.
In the West Bank, 14-year-old girl Malak al-Khatib was violently arrested on suspicion of throwing stones at a road used by Jewish settlers, HRW quoted her mother as saying.
"While on the ground, they kicked her and one soldier stepped on her neck."
In every case HRW documented, the Palestinian families said Israeli authorities "did not inform parents of the child's arrest and interrogated the children without permitting them to speak to a parent or lawyer prior to the interrogation".