[5] At the end of the 2015–16 season, Luton released Jake Howells, Alex Lawless, Paul Benson, Isaac Galliford, Scott Griffiths, Ryan Hall, Mark Onyemah, Luke Trotman and Curtley Williams.

[6] Matt Robinson was initially placed on the transfer list,[6] along with Mark O'Brien and Magnus Okuonghae,[6] before he was released one year early from his contract along with Elliot Justham one week later.

[10] Luton made eight summer signings, including goalkeeper Christian Walton on loan from Brighton & Hove Albion,[11] defenders Glen Rea from Brighton & Hove Albion,[12] Alan Sheehan from Bradford City,[13] Johnny Mullins from Oxford United,[14] midfielder Jake Gray from Crystal Palace,[15] and strikers Danny Hylton from Oxford United,[16] Jordan Cook from Walsall,[17] and Isaac Vassell from Truro City.

[25] The next match saw Luton play newly relegated Championship club Aston Villa at home in the first round of the EFL Cup, with the visitors taking the lead in the 13th minute through a scuffed shot by Jordan Ayew.

[27] McGeehan scored a penalty to give Luton a 62nd-minute lead at home to Newport County, before the visitors equalised eight minutes later through Jennison Myrie-Williams.

[28] After a challenge on Pelly Ruddock Mpanzu, McGeehan scored another penalty and Luton's second goal in second half stoppage time to secure a 2–1 win.

[29] After Olly Lee hit the crossbar, Matt Godden scored the winner in the 96th minute from a Tom Pett counter-attack, a result that saw them earn their first ever home win over Luton.

[32] Darren Oldaker scored a consolation goal for Gillingham in second half stoppage time, before Connor Tomlinson came on as a late substitute for Luton to become the club's youngest player to make his first-team debut at 15 years and 199 days old.

[38] Luton's unbeaten home record came to an end after a 2–1 defeat to Grimsby Town, who took the lead in the 29th minute through Omar Bogle, after a shot from Luke Summerfield rebounded into his path.

[49] This was followed by a 3–1 defeat at home to Millwall in the third and final EFL Trophy group stage match, in which Luton took the lead on 57 minutes when Mackail-Smith's cross resulted in an own goal from Shaun Hutchinson.

[50] Fred Onyedinma equalised for Millwall in the 71st minute from Gregg Wylde's cross, before two goals later in the second half from Harry Smith on his debut finished the scoring for the visitors.

[50] McGeehan scored in the 75th minute from a James Justin cross as Luton beat Accrington Stanley 1–0 at home to extend their unbeaten league run to eight matches.

[51] Luton were fined £15,000 by the English Football League after they failed to field a full strength team in each of their EFL Trophy group stage matches, deducted from the £20,000 prize money awarded after their opening two wins in the competition.

[52][53] Goalkeeper Liam Gooch joined Southern League Premier Division club Hitchin Town on a one-month loan.

[57] Michael Smith equalised four minutes later with a side-footed shot from 20 yards before Gareth Evans scored shortly before half-time after Luton failed to clear a corner.

[58] Midfielder Alex Atkinson joined Southern League Division One Central club Hanwell Town on a one-month youth loan ahead of the expiration of his contract at the end of December.

[59] Luton progressed to the third round of the FA Cup after a 6–2 win at home to Solihull Moors, in which the visitors were 2–0 up at half-time through two first half goals from Jamey Osborne.

[64] Striker James Verney joined Southern League Premier Division club Kings Langley on a one-month youth loan.

[67] Luton's first result of 2017 was a 1–0 defeat away to Portsmouth, whose goal came in the 31st minute when Christian Burgess converted Carl Baker's cross with a header.

[68] O'Brien left the club by mutual consent,[69] while midfielder Lawson D'Ath was signed from Northampton Town on a one-and-a-half-year contract, with the option of a one-year extension.

[70] Luton were knocked out of the FA Cup after losing 2–1 away to Accrington Stanley in the third round, in which the home team took the lead through Sean McConville in first half stoppage time.

[73] Luke Gambin, a Malta international, was signed from Barnet on a two-and-a-half-year contract, with the option of a one-year extension, for an undisclosed fee,[74] while McQuoid joined Stevenage on loan until the end of the season.

[78] Striker Geo Craig joined Isthmian League Premier Division club Hendon on loan until the end of the season.

[101] Zane Banton joined National League South club St Albans City on loan until the end of the season.

[103] Vassell scored a consolation goal for Luton in second-half stoppage time from close range after Colchester were unable to make a clearance.

[103] Palmer scored a 90th-minute winner for Luton from two yards at home to Blackpool in a 1–0 win, after goalkeeper Dean Lyness failed to hold Gambin's shot.

[106] Luton drew 2–2 at home to strugglers Leyton Orient, taking the lead in the 33rd minute through Hylton with his 25th goal of the season from Lee's through ball.

[109] Mpanzu put Luton in the lead in first half stoppage time with a shot into the bottom corner from 18 yards, the match finishing a 2–1 win.

[110] Justin scored his first professional goal to give Luton a 28th-minute lead away to Accrington Stanley, before the home team equalised six minutes before half-time through Matty Pearson with a header.