The 30-year-old was working in the shop on Station Road, Windygates, when a man entered and attacked her with a weapon before fleeing.
He reportedly waited for customers to leave before attacking the woman and left her with serious head injuries.
Officers said nothing was taken during the attack, which happened at about 18:00 on Friday.
The victim was treated at the scene by paramedics before being taken to the Victoria Hospital in Kirkcaldy.
Her attacker is said to be Asian and in his early 30s with thinning hair.
He was wearing a black bomber jacket and black trousers.
Det Insp Paul Dick appealed for witnesses. He said: "We are currently investigating this vicious attack and are eager to trace the man responsible as soon as possible.
"I would appeal to those who may have been either within the village shop or in the immediate area near to the time of the attack to come forward as they may have seen the man enter the premises or loitering about in the area around the time of the incident.
"I would urge anyone who has information, including those using public transport in the wider Fife area on Friday, February 3, to get in touch with police immediately."
Police are treating a "vicious attack" on a woman at a shop in Fife as attempted murder.