The rise in fentanyl use during pregnancy has introduced new and complex challenges in caring for women with opioid use disorders (OUD) and their infants diagnosed with neonatal abstinence syndrome or neonatal opioid withdrawal syndrome (NAS/NOWS). Despite the increasing prevalence of opioid-affected mother-infant dyads, limited research exists on healthcare providers’ perspectives regarding fentanyl’s impact on perinatal and neonatal care. This study aimed to explore the evolving challenges that fentanyl use has introduced to the care of perinatal women with OUD and their infants experiencing NAS/NOWS, from the perspectives of healthcare professionals. Fifteen healthcare providers—including neonatologists, obstetricians, nurse practitioners, registered nurses, and pediatricians—from the Pacific Northwest completed a qualitative online survey consisting of Likert-type and open-ended questions. Reflexive thematic analysis was applied to analyze open-ended responses. Three key themes emerged from the data, reflecting systemic shortcomings and barriers to effective, evidence-based care: (1) Systemic Barriers to Perinatal and Infant Care, (2) Impact of Increasing Polysubstance Use on Neonates and Mothers, and (3) Stigma and Judgment from Healthcare Providers Toward Perinatal Women with Substance Use Disorders. The findings underscore how interconnected systemic issues—ranging from healthcare infrastructure to societal attitudes—contribute to suboptimal care for mothers and infants amid the growing crisis of fentanyl and polysubstance use. These themes point to an urgent need for policy reforms, provider education, and integrated care models that can address the evolving and complex needs of these vulnerable families.