The following combinatorial proof may be of interest as well. After multiplying both sides by $(-1)^n$, and reindexing the summation by replacing $k$ with $n-k$, we can rewrite the equation to be proved as
$$
\sum_{k=0}^n(-1)^k\binom{n}k\binom{2n-k}n=1
$$
Both sides are answer to the following question:
How many strings of $n$ ones and $n$ zeroes are there were no zero is immediately followed by a one?
Obviously, there is only one such string, $11\cdots100\cdots0$.
On the other hand, we can count this using the principle of inclusion exclusion. Take all of the $\binom{2n}n$ strings of $n$ zeroes and $n$ ones, and for each $i=1,2,\dots,n$, subtract the strings where the $i^{th}$ zero is followed by a ones. Every such string can be generated by taking an arbitrary string of $n$ zeroes and only $n-1$ ones, then adding a one after the $i^{th}$ zero. Therefore, for each $i=1,\dots,n$, we must subtract $\binom{2n-1}n$, so subtract $n\binom{2n-1}n$.
However, strings with two instances of a zero followed by a one have been double subtracted, so these must be added back in. Using a similar method, the number strings where both the $i^{th}$ zero and the $j^{th}$ zero are followed by ones is $\binom{2n-2}n$. We must add this for each of the $\binom{n}2$ pairs of zeroes, so add in $\binom{n}2\binom{2n-2}n$.
Continuing in this fashion (subtracting in the triply subtracted strings, adding in the quadruply subtracted strings, etc), we recover the alternating sum on the left hand side.