A subsequence of a word $w$ is a word $u$ such that $u = w[i_1] w[i_2] \dots w[i_{k}]$, for some set of indices $1 \leq i_1 < i_2 < \dots < i_k \leq \lvert w\rvert$. A word $w$ is $k$-subsequence universal over an alphabet $Σ$ if every word in $Σ^k$ appears in $w$ as a subsequence. In this paper, we study the intersection between the set of $k$-subsequence universal words over some alphabet $Σ$ and regular languages over $Σ$. We call a regular language $L$ \emph{$k$-$\exists$-subsequence universal} if there exists a $k$-subsequence universal word in $L$, and \emph{$k$-$\forall$-subsequence universal} if every word of $L$ is $k$-subsequence universal. We give algorithms solving the problems of deciding if a given regular language, represented by a finite automaton recognising it, is \emph{$k$-$\exists$-subsequence universal} and, respectively, if it is \emph{$k$-$\forall$-subsequence universal}, for a given $k$. The algorithms are FPT w.r.t.~the size of the input alphabet, and their run-time does not depend on $k$; they run in polynomial time in the number $n$ of states of the input automaton when the size of the input alphabet is $O(\log n)$. Moreover, we show that the problem of deciding if a given regular language is \emph{$k$-$\exists$-subsequence universal} is NP-complete, when the language is over a large alphabet. Further, we provide algorithms for counting the number of $k$-subsequence universal words (paths) accepted by a given deterministic (respectively, nondeterministic) finite automaton, and ranking an input word (path) within the set of $k$-subsequence universal words accepted by a given finite automaton.