The shocking move comes as Scion was in the midst of a product renaissance and is characterized as a "leap forward for Toyota," according to the automaker.
The Scion tC coupe will be discontinued. Production ends in August.
The Scion C-HR, which debuted at the 2015 Los Angeles Auto Show in concept form and hinted at a new direction for the brand, will be part of the Toyota lineup.
He wrote that the end of Scion, "doesn't affect us day to day. We sell and market separately. We do plan a next-generation (BRZ)."
Toyota thanked its Scion dealers for cultivating younger buyers and serving as a test bed for the Japanese automaker.
"We appreciate our 1,004 Scion dealers and the support they've given the brand," said Bob Carter, Toyota senior vice president of automotive operations, in a statement. "We believe our dealers have gained valuable insights and have received a strong return on their investment. During this time of transition, we will work closely with them to support this process and help communicate this change to customers."
Toyota said customers seeking service and repair for Scion vehicles should "continue to visit Toyota dealerships' service departments."
Scion owners have an average age of 36, according to Toyota, one of the youngest demographics in the industry.
But Toyota said those buyers have a "different mindset" than when Scion first debuted and have "come to appreciate the Toyota brand and its traditional attributes of quality, dependability and reliability."
Toyota reported lackluster Scion sales in January.
The automaker sold 715 Scion tCs, a drop of 41 percent from a year ago; Scion FR-S sales totaled 507, a decline of 32 percent. It sold 1,250 Scion iMs and 1,840 Scion iAs in January. Both went on sale last fall.
Edmunds says: It was a noble experiment, but it's time for Toyota to move on.