Racial-ethnic and gender inequalities are well documented in Special Educational Needs and Disability (SEND) provision for Social, Emotional and Mental Health (SEMH) and mental health-related referrals, hospital admissions and service use. Understanding whether coordination between these systems differs systematically across groups is essential for identifying opportunities for equitable provision and access. Developed in partnership with peer researchers and community stakeholders, we examined cross-system pathways, between SEND-for-SEMH and mental health-related hospital contacts, based on gender and racial-ethnic group. Population-level analysis of ECHILD linked National Pupil Database and Hospital Episode Statistics for 1.7m children (ages 5–16) attending state schools in England (2005–2018). We examined rates, timing and risk ratios of pathways between systems. Substantial variation exists by gender, racial-ethnic group, and at their intersection. Nearly all girls were significantly less likely to receive SEND-for-SEMH following mental health-related hospital contact. Among girls with hospital contacts who never received SEND-for-SEMH, 49.8% had an inpatient admission. All pupils from Asian, Black African, Mixed Other, white Other and Other racial-ethnic backgrounds were significantly less likely to receive SEND-for-SEMH following hospital contacts. Conversely, Black Caribbean, Mixed white-Black Caribbean, Romani and Irish Traveller boys were recorded with SEND-for-SEMH at substantially higher rates and faster on enrolment. Linked administrative data reveals intersectional discrimination and systematic coordination failures not captured in single-system analyses. Findings demonstrate need for standardised mental health guidance and equity-oriented frameworks to address the persistent biases in system pathways as well as statutory integrated care pathway to address unmet need following in-patient hospital admissions.