[4] The losing streak was halted in the third match of the season when Everton defeated Wigan Athletic at Goodison Park, the game-winner coming in the form of a second-half, Leighton Baines penalty kick during injury time.

[5][6] The next match, in September, saw Everton take an early lead at Craven Cottage, but captain Phil Neville went down to a knee injury in the second half as the Toffees fell 2–1 to Fulham.

[9] Everton then returned to Goodison Park and, behind two goals from Louis Saha and one from Joseph Yobo, easily dispatched of Blackburn Rovers, 3–0.

The match did, however, see Lucas Neill's first start for the club, and he assisted on both of Everton's goals, which were scored by Louis Saha and Marouane Fellaini, respectively.

[20] This would however be Everton's last win in November with losses occurring against Manchester United, Hull City and Merseyside Derby rivals Liverpool.

In the game against Manchester United at Old Trafford, Everton were defeated 0–3 with goals from Darren Fletcher, Michael Carrick and Antonio Valencia.

Didier Drogba and Nicolas Anelka put Chelsea ahead but Yakubu drew the score in the fifth minute of first half injury time.

[30][31] Both teams played well, and Sunderland clung to a one-goal lead for much of the match after Darren Bent converted a header from Kenwyne Jones in the 17th minute.

In their final match of 2009, on 28 December, the Blues were able to end they calendar year on a positive note as they earned their first win in over seven weeks – and first victory at home in over three months – defeating Burnley at Goodison Park, 2–0.

Burnley manager Owen Coyle criticised the referee after the match, believing the Everton's go-ahead goal had been scored with Yakubu in an offside position.

[36][38] New American loanee Landon Donovan made his debut, harassing Arsenal defender Armand Traoré throughout the match – and tallied an assist in the 12th minute on a curling corner kick that was headed past Manuel Almunia by Leon Osman.

When it appeared that Everton were going to get their first win at Emirates Stadium, but a Tomáš Rosický shot deflected off Lucas Neill and into the twine as Arsenal were able to salvage the draw.

[43] Everton were unable to duplicate the FA Cup run of the previous season as they were eliminated by Birmingham City, 2–1, in front of their home crowd at Goodison Park.

[45][46] Everton qualified for the fourth round of the competition with a 4–0 victory away at Hull with goals from Jô, Dan Gosling, Leon Osman and Yakubu, who made his first start on return from his achilles injury.

[49] Everton, debuting their all-purple alternate kit, were eliminated from the League Cup in their second match, a 2–0 loss away to Tottenham Hotspur in the Round of 16.

[50][51] Everton opened play in the Europa League in the play-off round and were drawn against Czech club Sigma Olomouc,[52][53] who finished fourth in the 2008–09 Gambrinus liga.

[54] In the return leg in Olomouc, Tony Hibbert was sent off in the seventh minute, but Everton were able to hold strong, earning a 1–1 draw for the 5–1 aggregate victory.

[57][58] Everton then continued their perfect start to the group stage with a 2–1, come-from-behind victory over BATE Borisov, with goals from Marouane Fellaini and Tim Cahill cancelling out Dzmitry Likhtarovich's 16th-minute opener.

[66][67][68] In the Toffees' final group stage match, with several senior starters injured and the club having already secured passage into the knockout rounds, David Moyes fielded a young side against BATE.

[74][75] For the return leg, Everton's Nigerian contingent of Yakubu and Yobo were both initially denied entry into Portugal as a result of passport issues stemming from Portuguese foreign relations with Nigeria, but both players arrived via Amsterdam on the morning of the match.

Everton's hopes of forcing extra time remained alive after Pedro Mendes' 76th minute shot deflected off Jack Rodwell and into the net.