The Boro boss was picked ahead of Millwall's Kenny Jackett and Sean O'Driscoll of Nottingham Forest.
During October, Boro won five and drew one as they surged towards the top of the Championship.
It is Mowbray's third monthly prize since his return to the club and he was delighted to take the honour.
"It is a reflection of how well the club is doing, it is such a highly competitive game so to go through October is a reflection of the hard work of the staff and the players," he told Sky Sports News.
"There were some really good performances throughout the month, and we ate happy to keep the points tally ticking along.
"We have a good group and a good spirit and they are all doing their part."
Burnley's Charlie Austin capped his fine month by picking up the player's award.
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