Example. Let X = \text{Spec} k[x] and Y = \text{Spec} k(x). Then their function fields are canonically isomorphic (both being k(x)).
Claim. There is no rational map X \dashrightarrow Y.
Proof. Suppose we have a rational map f: U \to Y for some open dense subset U of X. Shrinking U if necessary (as all nonempty subsets of X are dense), assume that U = D(f). Thus f induces a morphism \varphi: k(x) \to k[x, 1/f]. Note that on stalks, this morphism should be identity \varphi_{\eta}: k(x) \to k(x), so \varphi must be identity on k[x]. This is impossible.
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For integral finite type k-schemes (in particular, irreducible varieties), morphisms of function fields do indeed determine rational maps between the schemes.
Proposition. Let X be an integral k-scheme and Y be an integral finite type k-scheme. Let \varphi: K(Y) \hookrightarrow K(X) be a k-homomorphism. Then there exists a dominant k-rational map \phi: X \dashrightarrow Y inducing \varphi.
Proof. The map \phi is equivalent to a map from a non-empty open subset of X to a subset Y sending the generic point \eta_X to \eta_Y. Moreover, as function fields of nonempty open subsets of X (resp. Y) are canonically isomorphic to K(X) (resp. K(Y)), we can assume Y = \text{Spec} B and X = \text{Spec} A are affine. We have a morphism \varphi: B \hookrightarrow K(Y) \hookrightarrow K(X).Warning: Clearly \varphi induces a morphism \text{Spec} \varphi(B) \to \text{Spec} B. However we do NOT have a way to take U = \text{Spec}\varphi(B) as an open subset of X.
So instead, we want to find some A_g \subset K(X) such that \varphi: B \hookrightarrow A_g. This would induce a map a map D(g) \to Y.
Why can we find such an A_g? This is because Y is a k-scheme of finite type. Thus B = k[b_1, \ldots, b_n] for some b_i's. Let \varphi(b_i) = a_i/f_i. Let g = f_1 \cdots f_n. Then as \varphi is a k-homomorphism, the image of B indeed lies in A_g.
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In particular if both X and Y are integral finite type k-schemes then a rational map X \dashrightarrow Y that induces isomorphism K(Y) \cong K(X) must be birational.
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