Bothroyd struck in each half - either side of a goal from Seyi Olofinjana.
It was a well-timed first win in five games for Mick McCarthy's side that had collected just one point from their previous four matches.
The finishing of Bothroyd, who started for the first time in 23 games, was the crucial difference between the two sides.
Hull, who have now lost three of their last four games, had chances of their own but Phil Brown's team lacked a cutting edge in front of goal and that proved to be costly.
Despite an improved second-half display, all they had to show for their efforts was a consolation strike on the hour when Nicky Forster scored his fifth goal of the season.
Trailing 2-0 at half-time, Hull's hopes of a comeback were all but extinguished just two minutes after the re-start when Bothroyd converted a cross from Andy Keogh.
Hull's spirits were raised briefly when Forster muscled his way past the Wolves central defender Gary Breen before beating Jan Budtz with a powerful drive but the damage had been done well before then as far as City were concerned.
Bothroyd's first goal was presented to him on a plate by a great pin-point cross from Michael McIndoe.
It would have been harder for the well-travelled Bothroyd to miss as he powered home a close-range header from ten yards.
The shock of falling behind sparked Hull into their best spell of the first half, but they could not find an equaliser as they were let down by their finishing.
Damien Delaney headed wide when well-placed, Ricardo Vaz Te was denied by a smart save from Budtz and then Forster missed the target after a neat pass from Dean Windass.
Those failings returned to haunt the Tigers seven minutes before half-time when Olofinjana grabbed his eighth goal of the season to make him Wolves' leading scorer.
Once again, Hull were caught out in the air after they failed to fully clear a corner.
The loose ball found its way to Michael Kightly who picked out Olofinjana and the Nigeria international buried his header from 12 yards at the far post.