The first club in the town of Barnet to play in the Middlesex Senior Cup was the original Barnet FC who used to play at Queens Road, the site of QE Boys's secondary school these days. They made their first appearance in the competition during the 1896/97 season when they were drawn to play away at Hanwell Town in the 1st round of the competition. Goals by Cocks, McLean & Gillespie gave Barnet a 3-2 win and they got as far as the 3rd round before losing 2-0 to the 3rd Grenadier Guards team at Queens Road.
Barnet's best performance in the competition was in 1898/99 when they reached the semi-final before losing 3-0 to West Hampstead at Tufnell Park's Caledonian Park. The team that day was; Marriott, Easton, Long, Maidman, Roach, McLeod, Janes, Davis, Prince, McGeorge, Cocks.
The last Middlesex Senior Cup appearance of the original Barnet FC was in 1900/01 and the club was hammered 7-2 by Olympic. The club went into liquidation in January 1902.
In 1904/05, Barnet Alston who had been originally known as Alston Works Athletic entered the Middlesex Senior Cup for the first time. However, the club lost at the first attempt, losing 6-1 to Hounslow Town after having drawn the original tie 2-2.
In 1905/06, Barnet Alston reached the 3rd round after beating Kildare in the 2nd round 1-0 but they went out at the next stage losing 4-2 to the 2nd Battalion Grenadier Guards.
However, there was another Barnet club playing in the competition that season. A second club with the name Barnet FC made their first appearance in the senior County Cup. The club were not a new club though; they had previously been known as Barnet Avenue and had dropped the Avenue part of their name in 1904. The club had been around since 1890 when they were known as Shrewsbury FC. They reached the 1st round proper of the competition before losing 2-1 to Harrow United. The match was played at Queens Road, which the Avenue club had taken over from the now defunct, original Barnet FC.
For the 1906/07 season, Barnet Alston moved over to playing in the London Senior Cup and those two seasons mentioned above were their only appearance in the Middlesex Senior Cup. However, Barnet FC continued in the Middlesex County Cup defeating Holborn 5-1 in the opening qualifying round with Harrison scoring a hat trick and Hawkins scoring twice. However, the club went out in the following round to Edmonton losing 2-0 in a replayed 2nd qualifying round tie.
For the 1907/08 season, Barnet FC applied to join the Southern Amateur League but there application did not get in on time and the club had to accept a place in the rather low level, Chiswick League instead. This was around the time of the breakaway Amateur Football Association and Barnet FC became one of it's members.
Barnet were drawn to play Mercians at Queens Road in the 2nd round of the competition but they lost 4-2 with goals from A Young and Dawe. The next few seasons, the club entered the Amateur Football Association Senior Cup and the match against Mercians was the last Middlesex County Cup game that this particular incarnation of Barnet FC would play.