A gale force wind and snowy conditions made any form of running rugby at The Showfield very difficult.
Stand-in skipper Ollie Roberts lost the toss to the strong opposition and the Maroons had to play downhill with the wind blowing from left to right.
Both sides' defensive displays were excellent all afternoon and the home side knew they were in for a tough game.
The visitors controlled the ball for 80% of the match and the Maroons had to live off scraps of possession.
But strong running by centre Dave Straker and Harry Pindar enabled the home side to move forward with Joe Quinn and Mark Parkin mopping up as much as they could around the park.
Whitby got the breakthrough they needed when a set penalty move enabled winger Pete Stentiford to score his 24th try of the year, breaking through the onrushing defence.
Straker kicked the conversion despite the strong wind.
The Maroons were on the back foot again but a cheeky interception by Stentiford out-witted the covering defence.
His cross kick was gathered well by youngster Chris Smith who fed the onrushing Ollie Roberts who burst clear.
The move temporarily broke down but was soon revived by Quinn and Parkin.
Phil Stentiford's pass was pushed down by the opposition winger and Ollie Roberts collected and rounded the defence to score out wide.
The kick was missed.
Harrogate bounced back when, after several phases of play and some penalties, their fly half slid through a covering defence to score under the posts.
The conversion was added despite an attempted charge down by Straker as the Ball squirmed through the uprights, but too late to stop the Maroons winning the contest.
The second half saw missed opportunities by the away side to score more points and the pressure they put Whitby under was immense.
Phil Stentiford and Chris Dobson made try-saving tackles and Matt Russell showed a strong presence. Whitby's defence held firm and was excellent all game.
Whitby won this game with grit and determination and go through to play York RI in the fourth round a week tomorrow.
If Maroons win that, they will play Hullensians of Yorkshire League Three in the quarter-finals.
Whitby Gazette man of the match: Matt Russell. Match sponsor: Wasley Chapmans.
* Maroons host Team Northumbria in the league on Saturday, 3pm kick-off.

Result: Whitby Maroons 12 Harrogate Pythons 7