In spite of the very real threat of war the preparations for the 1939/40 season went ahead as usual. The Football League started on schedule on 26 August with the Stags losing 4-5 at home to Crystal Palace. Two more matches were played (a 2-1 win at Watford and a two-all draw at Torquay) before Mr Chamberlain's radio broadcast on Sunday 3 September that declared ' consequently this country is at war with Germany'. In contrast to WW I the Football League cancelled its programme for the duration and the government announced a ban on the assembly of crowds until further notice. This ban did not last long before the realisation that the threat of air raids was not as bad as first suspected and a maximum attendance limit was imposed.
By October the Football League had organised regional competitions where clubs from all standards were grouped together. The rules regarding registration of players were relaxed so clubs in the proximity of bases for the forces relished this, Aldershot were able to turn out almost an English international XI! For the record the Stags first fixture was away at First Division Grimsby Town and they lost by 1-2. Incidentally one of the Mariners' goal scorers was Ted Roberts (a guest player from Coventry City) father of Dudley Roberts, a famous striker for the Stags 30 years in the future. The side, not surprisingly was unsettled throughout the season but Town still managed a creditable 5th placing in the table out of the 11 participating teams.
For the 1940/1 season the leagues were rearranged and Town were included in the South Regional League. As travelling was restricted all teams could not play every other and so the number of matches played by every team was not equal so league position was determined by goal average (goals for divided by goals against). Town finished in 17th place out of 34 with a goal difference of 1.132, having scored 77 and conceded 68 goals in their 29 matches. 'Tex' Rickards led the way netting 38 of the goals including a hat trick in just 3.5 minutes in the 6-2 beating of West Brom.
The following season the Stags joined 37 other clubs in the Football League North. In the first competition Town finished in a miserable 33rd place. In the secondary competition they were even worse, finishing in 50th place out of the 51 competing. Seven qualifying matches were played in the League Cup (a league competition, not a knockout), Town did not qualify for the later stages.
1942/3 was even more of a disaster with Town finishing bottom of the table in the first competition. There was no improvement at all in the second competition where another bottom place was secured. Once again they failed to qualify for the later stages of the cup competition finishing two off the bottom in the table. Somehow Middlesbrough and Oldham managed to finish lower than the dreadful Stags. In January Selby Musgrave , the club secretary, died. He was replaced by Herbert N Mee the famous football referee.
There was some improvement in 1943/4, things could hardly have been worse, with a final placing in the first competition of 18th out of 50 entrants. This improvement turned out to be temporary as Town slumped to 47th out of 50 for the second competition. Once again there was no progress from the qualifying competition of the League Cup. In July 1944 the team manager, Jack Poole, announced his resignation to take up the position of trainer at Notts County. Current first team captain Lloyd Barke took up his duties for the following season.
With Barke in charge Town ended the first competition in 38th place. It is interesting to note that Nottingham Forest finished 39th and Notts County bottom of the lot in 54th place. The second competition was more of a struggle as the Stags dropped to 55th out of the 60 competing teams this time round. Forest overtook the Stags this time but County managed only 59th place. As usual Town got no further than the qualifying competition of the war time cup. In May 1945 the former English international player Roy Goodall was appointed manager/secretary as Lloyd Barke's tenure in the job expired.
By the time the 1945/6 season got underway the war had been won. However with so many players still in the services league matches were still played on the regionalised basis. There were changes though, the old third divisions north and south were reformed from the 1939 standings. The Stags therefore played in the southern section, which was itself divided into north and south sections because of travelling restrictions. The first half of the season comprised the league matches, the Stags won only 3 out of the 20 and so became wooden spoonists. In the second competition, which was the qualifying competition for the Division 3 South Cup, Town finished 3rd but did not qualify for the semi finals as only the top two teams from each section went through. There was some semblance of the returning normality when the FA Cup was resumed. For this season only all ties up to the semi final stages were played on a home and away basis. In the first two rounds the Stags were paired with non league opposition, firstly Gainsborough Trinity were beaten 5-4 on aggregate (extra time was required in the second leg) and then Grantham lost 3-2 on aggregate in the second. In the Third Round Sheffield Wednesday drew a crowd of over 9,000 to the Mill for a 0-0 draw. Over 22,000 turned up at Hillsborough for the second leg to see the Owls triumph by five goals to nil.
So the war was over and for 1946/7 the Football League would restart with the Stags in the Southern Section of Division 3. The same fixture list was used as had been drawn up for the aborted 1939/40 season. The first three matches were far more fruitful than those of seven years before as Town won the first two versus Crystal Palace and Watford and then drew with Torquay. From then on in it was downhill all the way as Town performed terribly and finished bottom of the division, below Norwich City on goal average. At the Football League's AGM the Stags sought re-election, however, it was proposed that as this was the first season after the war and with so many players still in the services that all four clubs seeking re-election should be returned unopposed without putting the matter to a vote. This proposal was passed and the Stags lived to fight another day, although at the meeting they were transferred into the Northern Section. There was no FA Cup success either as Northampton were triumphant in the first round tie at the County Ground.
Back in what was traditionally thought to be the weaker of the two regional sections of the third division, the Stags faired particularly better than the previous term, finishing in a comfortable 8th place. There was also some excitement in the FA Cup as Town reached the Third Round, disposing of Wimbledon (then a non league outfit) and Oldham in the earlier rounds. Both were beaten by the only goal on their own grounds. In Round Three Stoke City were the visitors to Field Mill and they took the honours from a 4-2 score line. In common with most clubs the Stags average attendances were reached record proportions in what has become known as the 'post war boom', this term an average of 11,545 went through the turnstiles for each home game, the best being the 18,863 who attended Field Mill for the visit on Lincoln City.
There was no improvement in the 1948/9 campaign as Town managed a mid table position all season to finish in a no more than respectable 10th position. Once again the Third Round of the FA Cup was reached. Gloucester City (4-0) and Northampton Town (2-1) were beaten in the First and Second Rounds respectively. The Third Round brought an exciting tie at Deepdale against Preston North End, Tom Finney and all. In front of a crowd of 33,000 the Stags were a little unfortunate to go down by the odd goal in three. League attendances were on a par with the previous year as the average once again topped 11,000, 11,292 to be exact. Doncaster Rovers proved to be the most popular visitors with 16,749 attending the opening match of the season.
After the struggle of war, during which one Stag (Ivan Flowers) lost his life, the return to peace had seen Town return to some semblance of normality and with the crowds on the up the Club could look to the future with some optimism.