We explored the existence and application of standard operating procedures (SOPs) for pain management (PM) in German neonatal intensive care units (NICUs), and identified the factors associated with their application in practice. This study was part of the Safety4NICU project, a cross‐sectional survey conducted from 2015 to 2016. All 224 German NICUs were invited to participate, providing written consent from the head neonatologist and head nurse. We distributed questionnaires to the head neonatologist, the head nurse, and the NICU staff (physicians and nurses). We asked the head neonatologist whether written SOPs for PM existed, and we asked the staff whether these SOPs were applied in their daily routine. We received evaluable responses from 468 physicians and 1251 nurses from 76 NICUs. Of these 76 NICUs, the head neonatologists from 54 NICUs (71.1%) reported that written SOPs for PM exist. However, only 48.5% of the physicians and 53.7% of the nurses declared that these existing SOPs were also applied. We found various predictors for the existing SOPs as being applied, depending on the profession. For physicians, clinical training was important (OR: 2.482, p ≤ 0.05), while for nurses their working experience was a decisive predictor (OR: 1.265, p ≤ 0.05). For both, a high level of perceived cooperative norms between physicians and nurses increased the probability that SOPs for PM were applied, whereas a high bed turnover rate decreased that probability. According to the responses from head neonatologists, written SOPs for PM were common in German NICUs. However, if management strategies on pain existed, this did not mean that these were directly applied in the daily routine. Clinical training of the staff, the promotion of adequate interprofessional cooperation, as well as allowing time to deal with these SOPs might be all essential measures to strengthen the application.