This paper is a contribution to the general program of embedding theories of dynamical systems. Following our previous work on the stochastic embedding theory developed with Darses [C. R. Acad. Sci. Ser. I: Math 342, 333 (2006); (preprint IHES 06/27, p. 87, 2006)], we define the fractional embedding of differential operators and ordinary differential equations. We construct an operator combining in a symmetric way the left and right (Riemann-Liouville) fractional derivatives. For Lagrangian systems, our method provides a fractional Euler-Lagrange equation. We prove, developing the corresponding fractional calculus of variations, that such equation can be derived via a fractional least-action principle. We then obtain naturally a fractional Noether theorem and a fractional Hamiltonian formulation of fractional Lagrangian systems. All these constructions are coherents, i.e., the embedding procedure is compatible with the fractional calculus of variations. We then extend our results to cover the Ostrogradski formalism. Using the fractional embedding and following a previous work of Riewe [Phys. Rev. E 53, 1890 (1996); Phys. Rev. E 55, 3581 (1997)], we obtain a fractional Ostrogradski formalism which allows us to derive nonconservative dynamical systems via a fractional generalized least-action principle. We also discuss the Whittaker equations and obtain a fractional Lagrangian formulation. Last, we discuss the fractional embedding of continuous Lagrangian systems. In particular, we obtain a fractional Lagrangian formulation of the classical fractional wave equation introduced by Schneider and Wyss [J. Math. Phys. 30, 134 (1989)] as well as the fractional diffusion equation.