Background: Due to the increasing rate of children and families who require support from both youth welfare services and from mental health services, a solid cross-institutional cooperation is needed to provide coordinated and integrated help. Studies involving not only qualitative, but also quantitative information from both services regarding not only general, but also case specific views on cross-institutional cooperation and psychosocial needs are lacking. Methods: Hence, we collected data from n = 96 children and families who received support from youth welfare office (YWO) and child and adolescents psychiatry (CAP) simultaneously. In a longitudinal survey, we assessed the evaluation of case specific cross-institutional cooperation and psychosocial needs by employees of YWO and CAP as well as descriptive data (including psychopathology of children) over a 6-month period. Repeated-measures ANOVAs were conducted to assess the effects of time and institution (YWO/CAP) on employees' evaluation of case specific cross-institutional cooperation and psychosocial needs as well as children's psychopathology. Results: The data showed that generally YWO employees rated the case specific communication better than CAP employees. Furthermore, CAP employees estimated psychosocial needs higher than YWO employees did. The employees' evaluation of total case specific cross-institutional cooperation did not differ between the employees of both institutions; it further did not change over time. The case specific evaluations did not correlate between the case responsible employees of YWO and CAP. Conclusion: The data showed satisfaction with the case specific cross-institutional cooperation in general, but meaningful differences in case specific ratings between both institutions indicate the possibility and need for improvement in daily work and cooperation as well as in regulations and contractual agreements. The implementation of more exchange of higher quality and transparency will ensure smoother cross-institutional cooperation. Future research should pursue this topic to convey the need for further improvement in cross-institutional cooperation into decision-making processes and to evaluate the success of innovative projects in this field.