When to remove the tefillin on Mondays and Thursdays
On days that the Torah is read, it is customary not to remove the tefillin before the Torah is returned to the Aron Kodesh. These days include Mondays, Thursdays, Taniesim and Chanuka. In congregations where the Torah is returned only after the kadish following Uva Letzion, the tefillin should not be removed until the Torah is returned after kadish. There is an allusion in a pasuk to the idea of wearing tefillin when returning the Torah to the Aron Kodesh, as is written: "Their king [represented by the Torah] went before them and Hashem [represented by the tefillin] was at their head."
(סעיף יג וס"ק נז)