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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