We investigate the existence of positive solutions for a class of fractional differential equations of arbitrary order δ>2, subject to boundary conditions that include an integral operator of the fractional type. The consideration of this type of boundary conditions allows us to consider heterogeneity on the dependence specified by the restriction added to the equation as a relevant issue for applications. An existence result is obtained for the sublinear and superlinear case by using the Guo–Krasnosel’skii fixed point theorem through the definition of adequate conical shells that allow us to localize the solution. As additional tools in our procedure, we obtain the explicit expression of Green’s function associated to an auxiliary linear fractional boundary value problem, and we study some of its properties, such as the sign and some useful upper and lower estimates. Finally, an example is given to illustrate the results.