The club was re-established as Llanrug United for the 1945-1946 season, and they joined the Welsh National League - Division III (West). But unfortunately the following season, as a results of complaints that the 'Recreation Ground' playing area was to small, the club were resigned to join the re-established Bangor & District League, and the home fixtures were played at 'Parc Bailey'. On Christmas day 1946, Llanrug gained a famous local derby win by three goals to one against Llanberis, and at the end of that season Llanrug were crowned champions of the Bangor & District League.

There was no end to the ground problem, and the following season the club had to switch back to their very first home at Cefn Llwyd. At the end of the season the Alves Cup was won at the Oval, Caernarfon, by a margin of four goals to three against Nantlle Vale. A great feast awaited the players and officials after the match at Bryn Bras Castle.

One of the local stars of the period was the Llanrug centre forward Emlyn Jones, and in April 1949 he was invited for trials at Bolton Wanderers for the third time. At the end of the season, following a nil-nil result after extra-time at Farrar Road, Bangor the League Challenge Cup was shared between Llanrug United and Portdinorwic.

The following season Donald Kimlock Macdonald from Bangor was appointed player-manager. He was a native of Glasgow, and had vast experience of playing professionally in the Scottish National League with Dunfermline. The League Challenge Cup was won again, by a margin of four goals to one against Llandudno Reserves.

The name of centre forward Emlyn Jones was prominent again in January 1951, when he scored eight goals for Llanrug, in a demolition match of fourteen goals to nil against Bethesda, it is believed that this record still stands today.

The problem of having an adequate pitch to play on was on going major headache for the club. At the commencement of the 1951-1952 season the home fixtures were played at Pontrhythallt, on land owned by Tan'Rwylfa Farm. Unfortunately the pitched proved to be totally in-adequate, and the club switched there home fixtures to Dôl Helyg. This ground was considered to be one of the best on the North Wales Coast, but once more for some apparent reason the club had to move and play at Parc Rhôs the following season.

In October, 1953 the club could not find a suitable and adequate pitch to play their home fixtures, and as a direct result had to resign from the league. Local rivals Llanberis also resigned, the supporters numbers were scarce, its was thought at the time that the introduction of the sport television programme 'Grandstand' was keeping them all indoors on Saturday afternoons.

The club re-joined the Caernarfon & District League for the 1954-1955 season, but the following season, there was no team in the village of Llanrug. The club re-joined the league for the 1956-1957 season, but unfortunately as a result of a lack of interest and financial problems the Llanrug United Football Club resigned from the Caernarfon & District League at the end of the 1958-1959 season, there wasn't a team in the village thereafter for nine years, until the re-emergence for the 1968-1969 season.