The Student Services Department in Lower School tailors, personalizes, and coordinates academic and social-emotional services for each student and family. Using current evidence-based practices such as a Multi-Tiered System of Supports framework and a Positive Behavior Intervention System, students are supported in the development of the Flatbush Five: responsibility, kindness, respect, humility, and honesty. Supports include literacy remediation, resource room services, enrichment, counseling, teacher and parent consultation, psychoeducational screenings, Department of Education services such as speech therapy, occupational therapy, and counseling, Student Support Team meetings, and case management.

Remedial and resource room services utilize a variety of multi sensory techniques from programs such as Orton Gillingham, Fundations, Handwriting Without Tears and The 360 Thinking Executive Functioning Program. Special social-emotional programs are given by the guidance department in all grades, including "Tommy an Amy", social-emotional puppets geared towards first through third graders.

Programs include mindfulness, learning and maintaining healthy habits including nutrition and exercise, digital citizenship, developing self esteem, cultivating healthy friendships, learning ways to be an upstander, and improving executive functioning.