It means it took that long to build. This is apparent from the fact that they were challenging Christ's claim that He would build it in three days, when it's taken 46 years of work thus far.
From Barnes' Notes on the Bible
Forty and six years ... - The temple in which they then were was that
which was commonly called "the second temple," built after the return
of the Jews from Babylon. See the notes at Matthew 21:12. This temple
Herod the Great commenced repairing, or began to rebuild, in the
eighteenth year of his reign - that is, sixteen years before the birth
of Christ (Jos. 'Ant.,' b. xv. Section 1). The main body of the temple
he completed in "nine years and a half" (Jos. 'Ant.,' xv. 5, 6), yet
the temple, with its outbuildings, was not entirely complete in the
time of our Saviour. Herod continued to ornament it and to perfect it
even until the time of Agrippa (Jos. 'Ant.,' b. xx. chapter viii.
Section 11). As Herod began to rebuild the temple sixteen years before
the birth of Jesus, and as what is here mentioned happened in the
thirtieth year of the age of Jesus, so the time which had been
occupied in it was "forty-six years." This circumstance is one of the
many in the New Testament which show the accuracy of the evangelists,
and which prove that they were well acquainted with what they
recorded. It demonstrates that their narration is true. Impostors do
not trouble themselves to be very accurate about names and dates, and
there is nothing in which they are more liable to make mistakes.