The woman, in her 20s, was stabbed in her neck at 7.16pm in a shopping mall by a man also in his 20s, the Tokyo Metropolitan Police Department said.
Both were pronounced dead at a hospital within an hour, police said.
Broadcaster TV Asahi said the woman was a store clerk of the Pokemon Center in the building and the perpetrator was wielding knives in both hands.
Before Thursday's incident, police had received complaints from a person, believed to be the deceased woman, over alleged stalking, the Asahi newspaper reported.
Videos posted on social media showed shoppers running away from the site as ambulances converged on the building, located just a few hundred metres from the Ikebukuro terminal, one of the busiest train stations in Tokyo.
The store was crowded with apparently more than 100 customers, including many children and foreign tourists, before the sounds of falling shelves and a woman screaming "help!" could be heard, a witness who fled the scene told Asahi.
Pokemon Co, which operates about two dozen stores in Japan selling merchandise from the popular franchise, said the store in Ikebukuro and its adjacent Pikachu Sweets cafe would be closed until further notice.
"We will prioritise our full co-operation with the police and our staff's physical and mental care," the company said in a statement on its website.
Strict gun controls in Japan mean knife attacks are a more common form of public violence, with multiple stabbing incidents on trains and at railway stations in the past few years.
