Preterm infants are exposed to numerous environmental stressors during their Neonatal Intensive Care Unit (NICU) stay, particularly during the first week after birth. The aim of this study is to assess whether salivary cortisol levels are correlated with Neonatal Infant Stressor Scale (NISS) scores in preterm infants during the first week of life. We also quantified the changes in both NISS scores and cortisol levels in the first week, and whether cortisol levels are associated with gestational age. Preterm infants (n = 38, birth weight <1250 g and/or gestational age <29 weeks) were included. Saliva samples were collected on day 0-3 (early) and day 4-7 (late), and cortisol concentrations were measured by immunoassay. NISS scores were assessed retrospectively for the six hours preceding each saliva collection. NISS scores were not significantly correlated with salivary cortisol levels at either time point. However, infants born at <28 weeks gestation had higher median cortisol levels than infants born at >28 weeks (p = 0.0068), and there was also a significant inverse relationship between NISS score and gestational age (p = 0.04). There was no significant difference between the early and late time points for either NISS scores or cortisol levels. Cortisol levels are elevated in infants <28 weeks gestation but do not correlate with NISS scores. NISS scores are inversely related to gestational age, likely reflecting increased exposure to interventions and invasive procedures for the smallest infants.