$\newcommand{\Z}{\mathbf{Z}}\newcommand{\Q}{\mathbf{Q}}$Yes for $n\ge 6$. Indeed, let $A$ be a matrix in $\mathrm{SO}(n,\mathbf{Q})$. First, if $Ae_i=e_i$ for some $i$, there is nothing to do, and if $Ae_i=-e_i$, say for $i=1$, multiplying $A$ with the diagonal matrix $(-1,-1,1,\dots,1)$ allows to conclude.
Write $Ae_1=(x_1,\dots,x_n)$. If $x_1=\pm 1$, we are thus done. Otherwise,
$\sum_{i\ge 2}x_i^2$ is a positive rational, hence sum of $4$ squares $y_2^2+\dots+y_5^2$, and Witt's theorem ensures that there is some element of $\mathrm{O}(n-1)(\mathbf{Q})$ mapping $(x_2,\dots,x_n)$ to $(y_2,\dots,y_5,0,\dots,0)$. Hence composing $A$ with an element of $\mathrm{SO}_n(\mathbf{Q})$ mapping $e_1$ to $\pm e_1$ yields $A'$ mapping $(x_1,\dots,x_n)=Ae_1$ to $(x_1,y_2,\dots,y_5,0,\dots,0)$. Using $n\ge 6$ and again Witt's theorem, we find an element of $\mathrm{SO}_n(\mathbf{Q})$, mapping $e_n$ to $\pm e_n$ mapping $A'Ae_1$ to $(1,0,\dots,0)$.
Edit: It is also true for $n=5$. As in the previous case, the point is showing that every orbit of the given subgroup (the subgroup $H$ generated by basis element stabilizers) in the rational 1-sphere meets an element with a zero coordinate.
Start from a tuple $(n_1,\dots,n_5)$ with $\sum n_i=1$. First suppose that all $n_i$ belong to $\Z_2$. Modulo 4, each $n_i^2$ is $1$ or $0$, hence either all are odd, or a single one, say $n_1$, is odd. If all are odd, all are $1$ modulo $8$, and we have a contradiction. So a single one is $1$. Then $n_1^2+n_2^2+n_3^2+n_4^2$ is equal to $1$ modulo $4$, hence, by Legendre's theorem, is a sum of 3 squares, and hence we can conclude in the same way as we did in the case $n\ge 6$ using Witt's theorem: the $H$-orbit of $(n_1,\dots,n_5)$ meets an element with a zero coordinate.
Otherwise, some $n_i$ is not in $\Z_2$. Let $2^k$ be a common denominator in $\Q_2$ for the $n_i$. Write $m_i=2^kn_i$. Then $\sum m_i^2=4^k$, the $m_i$ are in $\Z_2$ and not all even. Modulo $4$, since the $m_i^2$ are all $0$ or $1$ and sum to $0$, we deduce that exactly four of the $m_i$ are odd, say $m_5$ is even.
Then $(m_1^2+m_2^2+m_3^2+m_4^2)/4$ is a positive element of $\Q\cap\Z_2$, hence is a sum of 4 squares in $\Q\cap\Z_2$, namely $q_1^2+q_2^2+q_3^2+q_4^2$. Write $q_5=m_5/2$ Hence using Witt's theorem, $(m_1,m_2,m_3,m_4,m_5)/2^k$ is in the $H$-orbit of $(q_1,q_2,q_3,q_4,q_5)/2^{k-1}$. Arguing by induction on $k$, each orbit in the rational 1-sphere contains an orbit contained in $\Z_2^5$, and we are done.
This completes the picture, since the answer is a trivial no for $n=2$ and is also no for $n=3,4$ (see this answer and this answer).
To summarize, for $n\ge 6$ we used the fact that any positive rational is a sum of 4 rational squares, and for $n=5$ we used the fact (Legendre) that every positive element of $\Q\cap\Z_2$ that is $1$ modulo 4 is a sum of 3 squares in $\Q\cap\Z_2$. (The latter follows from the same statement in $\Z$, just multiplying by an odd square.)