Background: Addressing children's tobacco smoke exposure (TSE) remains a public health priority. However, there is low uptake and ineffectiveness of treatment, particularly in low-income populations that face numerous challenges to smoking behavior change. A multilevel intervention combining system-level health messaging and advice about TSE delivered at community clinics that disseminate the Special Supplemental Nutrition Program for Women, Infants and Children (WIC), combined with nicotine replacement and intensive multimodal, individual-level behavioral intervention may improve TSE control efforts in such high-risk populations. Methods/Design: This trial uses a randomized two-group design with three measurement points: baseline, 3-month and 12-month follow-up. The primary outcome is bioverified child TSE; the secondary outcome is bioverified maternal quit status. Smoking mothers of children less than 6 years old are recruited from WIC clinics. All participants receive WIC system-level intervention based on the "Ask, Advise, Refer (AAR)" best practices guidelines for pediatrics clinics. It includes training all WIC staff about the importance of maternal tobacco control; and detailing clinics with AAR intervention prompts in routine work flow to remind WIC nutrition counselors to ask all mothers about child TSE, advise about TSE harms and benefits of protection, and refer smokers to cessation services. After receiving the system intervention, mothers are randomized to receive 3 months of additional treatment or an attention control intervention: (1) The multimodal behavioral intervention (MBI) treatment includes telephone counseling sessions about child TSE reduction and smoking cessation, provision of nicotine replacement therapy, a mobile app to support cessation efforts, and multimedia text messages about TSE and smoking cessation; (2) The attention control intervention offers equivalent contact as the MBI and includes nutrition-focused telephone counseling, mobile app, and multimedia text messages about improving nutrition. The control condition also receives a referral to the state smoking cessation quitline. Discussion: This study tests an innovative community-based, multilevel and integrated multimodal approach to reducing child TSE in a vulnerable, low-income population. The approach is sustainable and has potential for wide reach because WIC can integrate the tobacco intervention prompts into routine workflow and refer smokers to free evidence-based behavioral counseling interventions, such as state quitlines.