to record their second Toolstation Northern Counties East League Premier Division win in four days.
Manager Marcus Newell made one change to the starting eleven which beat Athersley Recreation at the weekend with Miles Fenty replacing the unavailable Jody Barford in goal.
Cleethorpes began brightly and took the lead after just four minutes. Marc Cooper did well to beat defender Joe Danby to the ball on the right hand side before setting up Brody Robertson who fired the ball into the corner of the net to register his first goal of the season.
Pickering responded with a period of sustained pressure, the hosts knocking the ball around nicely but ultimately offering little threat in the final third. Striker Nathan Kamara came closest to equalising but blazed the ball high and wide from 20 yards as Pickering struggled to break through the resolute Owls defence.
The home supporters were screaming for a red card after 13 minutes as Tim Lowe was involved in an off the ball incident which left Pickering striker Callum Ward poleaxed on the floor. Somewhat fortunately for Clee, Lowe escaped with a yellow card.
Danny Trott came close for the Owls just moment later, sliding in to meet Robertson's cross but just failing to connect with the goal at his mercy before Cooper twisted and turned inside the penalty area before shooting straight at goalkeeper Peter Lawrie.
Fenty was forced into his first save of the game after 31 minutes, diving low to deny George Bissett. The Pickering winger came even closer just seconds later, hitting a piledriver from the right hand side which beat Fenty but rebounded to safety off the post.
The Owls made the home side pay for this miss as the visitors doubled their lead after 35 minutes. Lawrence Heward rose magnificently to meet Peter Winn's crossed free kick, powering his header past Lawrie and into the roof of the net.
The Owls had a lucky escape right on the stroke of half time as Bissett's cross hit the top of the bar.
Luke Mascall had the first opportunity of the second half, seeing his close range header saved by Lawrie.
Pickering continued to enjoy plenty of possession but were still struggling to trouble Fenty, mostly being reduced to long range efforts which were going high and wide, much to the frustration of the home supporters.
At the opposite end, Cooper headed an effort over the bar before Trott shot wide when well placed. The Owls were then denied by the woodwork themselves as Cooper lashed in a shot from the right hand side which thudded against the base of the post.
The game was then held up for five minutes as Pickering's Ward sustained a nasty injury in a collision with Fenty, the striker eventually leaving the field on a stretcher before being taken away in an ambulance.
Pickering came close to reducing the arrears after 70 minutes as a long cross from Matty Turnbull was missed completely by Bissett when he seemed certain to score.
Cleethorpes wrapped up the points in injury time as nice build up play involving Mascall, Caine Winfarrah and Alex Flett presented an opportunity to Cooper who sidefooted the ball past Lawrie.
The game came to an end seconds later and the Owls could reflect on a good victory on the road, three points and a clean sheet were suitable rewards for their endeavours.
The win moves the Owls up to 16th place in the league table, but now notably in touch with the teams at the top end of the table after a slow start to the season. Cleethorpes are next in action on Saturday when Garforth Town visit the Bradley FDC. Kick off will be at 3pm.