Netanyahu's coalition relies for its survival on two ultra-Orthodox parties that regard longstanding conscription exemptions as key to keeping their constituents in religious seminaries and away from a melting-pot military that might test their conservative customs.
The ultra-Orthodox conscription waiver has become especially charged as Israel's armed forces, made up mostly of teenaged conscripts and older civilians mobilised for reserve duty, are overstretched by a multi-front war, in Gaza and Lebanon.
"At the height of a difficult war, the burden of inequality is more than ever acute," the court's unanimous ruling said.
Most Israelis are bound by law to serve in the military, whereas ultra-Orthodox Jewish seminary students have been largely exempt for decades.