Almost always, these are two different actions.
The monodromy action is by path lifting, lifting a given path at each of the points in the fiber and mapping each such point to the endpoint of the corresponding lift. This makes sense for any covering space $q:(Y,y_0) \to (X,x_0)$, where $Y$ is possibly disconnected.
To get a well-defined action by the deck group $G=G(\widetilde{X})$, which can be identified with $\pi_1(X,x_0)$ in the universal cover $p:(\widetilde{X},\widetilde{x}_0) \to (X,X_0)$, on the fiber of an intermediate connected normal cover $q:(Y,y_0) \to (X,x_0)$, certain elements need to identified: $G(Y) \cong G/N$, where $N= q_*\pi_1(Y,y_0)$. So, there is an action of $G$ on $F = q^{-1}(x_0)$ that factors through the action of $G/N$ on $F$.
Here's an example where these two actions are different:
Let $X = S^1 \vee S^1$ with oriented labeled edges $x$ and $y$, identified with generators of $\pi_1(X)$. And let $Y = \widetilde{X}$ be its universal cover, viewed as a graph (4-valent tree) with labeled oriented edges and its vertex set identified with $\pi_1(X)$.
Consider the pair of adjacent vertices $(1,y)$. The monodromy action by the element $x$ sends this pair to $(x,yx)$, which are not adjacent in $Y$.
The deck group action by the element $x$ sends the pair to $(x,xy)$.
In general, the deck group action extends to a homeomorphism of $Y$. But the monodromy action need not extend continuously.
The above example is related to other actions: if $Y$ is a normal covering graph with fundamental group $N \trianglelefteq G$, where $G$ is a free group, then $Y$ is the right Cayley graph of the presentation $G/N$. The action of $F/N$ by deck transformations is the left action (by graph automorphisms). The monodromy action is the action on the vertex set by right multiplication (which does not extend to an action by graph automorphisms).
Exercise #27 in Chapter 1 of Hatcher's Algebraic Topology book is worth a look.
