Sydney Corcoran said her service dog, Koda, helps her deal with post-traumatic stress after she was injured in the attack in April 2013. Her mother lost her legs in the twin explosions.
"He's crucial to my everyday life," she told WCVB.
She had Koda with her when an employee at the T.J. Maxx in Nashua, N.H., told her to put the dog in a cart or leave.
"He had on his service dog vest -- bright blue, says 'service dog' all over it," Corcoran said. "The store manager came over to me and said to me, 'If you want to keep your dog in the store, you have to put him in the carriage.' "
She said the manager eventually apologized to her after she explained Koda's purpose, but she said "That's not good enough."
"There are so many people with invisible, silent injuries," Celeste Corcoran, Sydney's mother, said. "And the public needs to be aware that their service animals are sometimes their lifeline."
T.J. Maxx issued a statement apologizing for the incident and said it planned to make sure employees are informed about store policy allowing service animals.