The Czech player had reached the quarter-finals at Devonshire Park after saving match points in victories over British players Harriet Dart and Jodie Burrage.
"I'm very sorry to have to withdraw from my QF today in Eastbourne as I'm having some soreness in my right thigh," the 29-year-old Krejcikova said on social media.
"I've truly enjoyed my time down here the past week and loved being back on the grass."
Krejcikova looked to be moving okay against Burrage, but with the defence of her Wimbledon crown beginning on Tuesday, she has taken the decision to fully recover.
Her withdrawal means French qualifier Varvara Gracheva is in the semi-finals.