I am not sure that I understand what you mean by "I want to pass ODEs as a constraint to fmincon." What about the ODE solution is a constraint? Do you want the minimum value of the solution to be above zero? Do you want the ODE solution to lie in a certain box? Once you explicitly define what you mean by the ODE solution is a "constraint," then I think that the answer to your question will be obvious. You will solve the ODE, get sol, and then write the constraint in terms of sol, maybe fun(deval(sol,tspan)) for some appropriate function fun and set of times tspan.