Lynn appointed Paul Todd as manager for the 1953-54 season. Born in Middlesborough and based with the RAF in Doncaster during the war he was also captain of the RAF Command team in Ceylon. In his first season with Doncaster he scored 26 goals from 44 appearances. He went on to play for Blackburn Rovers and Hull City before joining Lynn.
Lynn were ambitious and, from the start, the season was looked upon as Lynn's last in the Eastern Counties League and it was important that Lynn should finish as high in the league as possible and ideally be financially successful.
Paul Todd made nine new signings – amongst these were Peter Robinson the Notts County wing-half and Tommy Reynolds – nicknamed “Titch” because he was 5 feet 4½ inches tall. He had spent seven seasons with Sunderland and prior to that had been with Todd in Ceylon. Former manager Jack Howe remained with Lynn as a player as the club's professional strength rose to twenty.
The first public trial march before the start of the season attracted a crowd of 2,476.
The results from Lynn's first eight league games were the worst since 1948 and the first away win in the league did not come until November and by that time Lynn had been removed from the FA Cup – going down at the first hurdle against March Town having had Morris sent off in the first half.
In terms of changes at the ground – rooms for the Supporters Club and a medical room were erected near the Tennyson Road entrance. Approval for covering the hospital end of the ground was given by the Council in December.
Although Treasurer Harry Graven had reported in October that there was “a bit of money in the bank” and the club had cleared outstanding accounts of £1,000, in January 1954 the Supporters' Club were asked for financial aid and gave £500, bringing the total for the season to £950.
Despite only drawing against Lowestoft Town on 9th January 1954 it was the start of an unbeaten run of sixteen league matches including a victory away to Harwich, their first league points there since 1909, it was 17th time lucky.
Lynn, unbeaten at home in the league, reached the top of the table for the first time with a victory over Crittalls Athletic in February whilst Terry Ryder recoded a 17 minute hat trick against Norwich City A.
Lynn wanted to progress to a higher league but which one?
“The Committee have given careful consideration to the question of entry to the Southern League, and in view of the travelling and certain circumstances, hotel expenses included, and also taking into account the additional expense, it has been agreed that application for entry to the Southern League be withdrawn” is was reported in the press. One alternative was to apply for membership of the Midland League which the club did, although they were aware that not all fans wanted this. When Lynn entertained Crittals Athletic in April 1954 fans were asked to vote for which league Lynn should play in the next season, either Midland or Eastern Counties. The match was attended by 3,888 (plus season tickets holders) but only 2,041 voted with the Midland League winning by a majority of 295.
Lynn reached the final of the Norfolk Senior Cup where they drew 0-0 with Yarmouth at Carrow Road in front of 14,261. They won the replay at The Walks in front of a more modest 5,909 but the Cup presentation was not without controversy. The presentation was made by Mr W R Masterson who, as well as being chairman of the Norfolk FA was also a Yarmouth supporter. In addition to not shaking hands with the Lynn players he also referred to the “tragic circumstances” in which the cup had been won – basically Yarmouth having to field some reserves players. It was left to Lynn manager Paul Todd to make mention of Lynn also having to call on reserves.
Lynn were assured of the league title on 24 Apr with a 3-0 win over Harwich having already won the league cup – defeating Lowestoft over two legs. Lynn were undefeated in the East Anglian Cup – the final against Barking was not played.
Lynn Reserves also had success in a season which saw a 20 match unbeaten run. Honours received were the Norfolk Intermediate Cup, the Peterborough League, Peterborough Senior Cup and the Adderley House Cup.
The Supporters' Club decided that plans to install covered accommodation at the Hospital end of the ground were impracticable and the Supporters Club proposed covering the entire length of the north side of the ground which would provide cover for 3,000 - 4,000
Lynn played 52 games with Paul Todd being ever present. Other leading appearances were Rowe on 51, Comerford, Reynolds, Ryder 49; Morris 45, Robinson, Taylor 44; Williams 40; Heagren 36.
Leading scorers: Ryder 41, Todd 36, Reynolds 25 (inc 8 pens), Heagren 15, Hutchinson 14, Morris 11, Whitelun 8, Wilson 2, Comerford and Spencer 1. Own Goals 4. Total 158.