Newborn screening for cystic fibrosis enables early diagnosis and treatment, leading to better outcomes for patients with cystic fibrosis. Although the sensitivity of several screening protocols is high, false negative screening results of the newborn patient still occur, which can lead to a significant delay in diagnosis when the awareness for presenting symptoms of cystic fibrosis declines. Neonatal cholestasis is one of the presenting symptoms of cystic fibrosis but can be easily missed when total parenteral nutrition has been given. Premature newborns are probably more at risk of a missed underlying diagnosis than term babies because their co-pathologies and management are often more complex. We present a case of a 10-week-old premature boy with a false negative newborn screening for cystic fibrosis, in whom cystic fibrosis presented with neonatal cholestasis. In this case, the immunoreactive trypsinogen/pancreatitis-associated protein/35 cystic fibrosis transmembrane regulator mutation analysis/sequencing method was used. Furthermore, an overview of the literature on missed diagnosis of cystic fibrosis due to a false negative newborn screen is provided. Conclusion: Cystic fibrosis (CF) should be considered in infants with neonatal cholestasis even when the newborn screening for CF is reported to be negative.