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.
"I think it's better with Wimbledon in the next couple of days just to rest it and to see what's going on and to resolve that," added Krejcikova, whose season has been blighted by a back injury which has limited her to a handful of matches.
Her withdrawal means French qualifier Varvara Gracheva is in the semi-finals, where she will face fellow qualifier Alexandra Eala, who beat Dayana Yastremska 6-1, 6-2 to become the first Filipino woman to reach a Tour-level semi-final on grass.
Maya Joint became the first Australian woman to reach an Eastbourne semi-final in 14 years after she backed up her impressive win over Emma Raducanu by beating Anna Blinkova 6-4, 7-5.
She will face Anastasia Pavlyuchenkova, who later beat Kamilla Rakhimova 6-2, 2-6, 6-0.