To test whether implementing a nursing-driven comfort protocol standardizes morphine use in one neonatal intensive care unit (NICU) and to examine how non-standard morphine (N-SM) relates to days of ventilation, days of total parenteral nutrition (TPN) and length of stay (LOS). This was a retrospective/prospective observational study using pharmacy records, medical records, and an outcomes database. Comfort protocol implementation began February 2011 and was applied to preterm, ventilated neonates <1500 grams. Pre- and post-implementation proportions of N-SM days were compared using the binomial test. A percent 'P'-chart spanning 30 quarters was constructed with statistical-process control analysis. Multivariable linear regression adjusting for acuity assessed the relationship between N-SM use and days of ventilation, TPN and LOS. Hundred and thirty-four patients met inclusion criteria, 116 prior to and 18 after implementation. The proportion of patients given N-SM for one or more days decreased from 59 to 35% after protocol implementation (P = 0.017). A 9-month period of decreased N-SM days was observed after protocol implementation. Controlling for acuity, each additional day of N-SM use was associated with 0.47 more days of ventilation (95% confidence interval (CI): 0.26-0.69, P < 0.001) and 0.52 more days of TPN (95% CI: 0.35-0.68, P < 0.001). Exposure to N-SM was associated with 17 additional days of hospitalization (P = 0.009, 95% CI: 4.5-30). Implementing a nursing-driven comfort protocol significantly reduced N-SM use. N-SM in the NICU is negatively associated with key clinical outcomes. Testing similar protocols in other settings is warranted.