The Skipton team also appeared five times in the final of the Yorkshire Challenge Cup or "T'owd Tin Pot" as it is affectionately known, between 1903 and 1912. The first appearance against Castleford in the 1902-03 Season, was not the happiest of clashes leading to a storm of controversy. The final played at Harrogate on 18th April, 1903, was a drawn game, the replay scheduled a week later at Belle Vue, Wakefield. The controversy arose when Castleford decided to play J. T. Taylor, an International three quarter back from West Hartlepool in the replay. A written protest was handed to the referee by Alec Ross the Skipton Captain, before the kick off, stating that they did not consider Taylor to be a bona fide member of the Castleford Club, within the rules of the Competition. The match, however, was played, the Castleford side including Taylor, who scored the winning tries, Skipton being beaten 6 points to nil. The Cup was presented to the Castleford Captain after the match, and Ross in his reply speech, stated that he did not consider Skipton had been beaten by a representative Castleford side. Nor apparently did the Yorkshire Committee who met the following Monday, and unanimously decided that Taylor was not a bona fide member of the Castleford Club, and ordered the match to be replayed. Castleford refused to replay the match, on the grounds that they considered the trophy had been fairly won. The Yorkshire Committee was unmoved and unanimously decided the Cup should be awarded to Skipton. There remained some, controversy about Castleford having had the Cup inscribed, and when it finally arrived at Skipton, it was found to contain 15 dumb tits, presumably the last derisive fling by the Castleford side who felt they had been unjustly deprived of the trophy.

Castleford were to have their revenge however, when the two Clubs met again in the final in April, 1908 when they beat Skipton 29 points to nill. The bitterness about the incident remained, and for many years afterwards, the fixture against Castleford "was always a bloodbath", as an older member describes it. Happily time heals all, and the Clubs now meet in friendly rivalry in the true spirit of the game.

Skipton won the Yorkshire Cup in the 1903-04 Season, when they beat Mytholmroyd by 3 points to nil, in the final played at Harrogate in April, 1904.

Skipton were to be involved in another unfortunate controversy when they played Headingley in the final in April, 1909, at Ilkley. There was no score up to five minutes before half time, when the ball was touched down for Headingley by Dobson. It was alleged by the Skipton Captain Bob Duckett that the ball had been over the dead ball line when it was touched down, and Duckett pointed this out to the referee, Mr. R. C. Bell. Mr. Bell apparently did not take any notice, saying, "I shall give a try here" , it was said that he then added that if the decision did not suit the Skipton Captain he could leave the field. The upshot was that in the excitement of the moment, Duckett did just that, and led his team off the field. The referee signalled that the match was over, and there were wild scenes as spectators invaded the pitch. Mr. Bell having to be escorted from the field by the police. The controversy continued to rage in Yorkshire Rugby circles. It was considered unsportsmanlike of the Skipton team to leave the field, and the incident was regretted by all, probably most of all by Duckett himself, who in leading his team from the field, had destroyed any chance of Skipton winning the match in the second half, when the wind and slope would have been in their favour. The Yorkshire Committee awarded the Cup to Headingley, and considered banning Skipton, from future competitions. They decided, however, thatthere had been a little unfairness towards Skipton, who had to change at a public house 1/2 mile from the field, and that the referee had cautioned the Skipton players before the kick off, whilst saying nothing to the Headingley team. These had the fact that a Skipton Player, Horner had been sent off without a prior caution, had all contributed to a feeling by the Skipton side that they were being discriminated against in favour of Headingley, and the final regrettable remark by the referee had been the "last straw" as it were.

Skipton did not reach the final in the next two seasons, but met Otley in the final in April, 1912 again at Ilkley. This time Skipton won the match 7 points to nil, and the Yorkshire Cup came to Craven for the third time in 10 years. Up to this time, a trophy of a silver rugby ball had been presented to the runner up in the Cup Final. To mark Skipton having won the Cup on three occasions the first team ever to do so, the silver football trophy was presented to Skipton outright. The Captain on this occasion was C. (Kit) Tosney, who was later an England International Trialist in 1920, and was capped for Yorkshire a total of 31 times between 1908 and 1920.

In all their appearances in the final of the Yorkshire Cup Skipton were very well supported by Skiptonions who travelled to the final wherever it was on Special Excursion trains. The return of the team was always greeted with wild enthusiasm, and on the occasions when the team was triumphant, they were met at the railway station by the local brass band, who preceded them on a tour round the principal streets to the Town Hall where they were welcomed by Civic Dignitaries. The evenings were usually rounded off by celebrations at the Club's Headquarters.

The silver football was a much prized possession of the Club, it was valued then at £50, and during the year was kept at the Grammar School, being brought to Social Functions occasionally. The very shape of the trophy was sufficient to suggest a "game" and on the occasions when high spirits prevailed, the Club was faced with minor bills for repairs to it. It remained in the possession of the Club until 1948 when the Committee decided that it should be returned to the Yorkshire R.F.U. to again be awarded as runner up trophy in the Challenge Cup Final. Ironically Skipton became first holders when they were defeated by Harrogate in the final held April, 1949.
Skipton made their sixth appearance in the final of the Yorkshire Challenge Cup, when they met Harrogate at Otley in April, 1949. Harrogate won the match 20 points to 6, and Skipton became first holders of the silver football trophy which they returned to the Yorkshire R.F.U. the year before. The Skipton team were well supported, 14 coach loads of supporters, and a well patronised excursion train making the journey to Otley. Red rosettes were being sold at Skipton railway station by local boy scouts in aid of the local Bob a Job fund, evidence of the "Cup tie fever" which existed in the town. The team were welcomed back by the Chairman of Skipton U.D.C. and entertained to dinner at the Devonshire Hotel. The following season the Club reached the semi final of the Cup, being beaten in the replay by Halifax.