APOEL's consolation goal came in the final minute of added time when a shot from Georgios Efrem deflected off Nuno Lopes' back to turn the ball past his own keeper.

On 18 September 2016, APOEL maintained their perfect start by beating Anagennisi Deryneia 2–0 at home, following second half goals from Belgian striker Igor de Camargo and a strike from distance from Brazilian winger Vander.

On 21 September 2016, in the first matchweek game which was postponed and rescheduled, APOEL dropped their first points of the season after being held to a goalless draw by Anorthosis at Antonis Papadopoulos Stadium.

Alex da Silva gave Apollon the lead midway through the second half after converting a penalty, but Facundo Bertoglio scored a last-gasp equalizer with a close range diving header to rescue a point for APOEL.

On 21 December 2016, in the last match of the year, Igor de Camargo's 47th-minute header was enough for APOEL to beat Nea Salamina 1–0 at home and move up to second place, two points behind AEK Larnaca.

On 14 January 2017, APOEL beat Doxa Katokopias 2–0 at Makario Stadium thanks to a first half goal from Igor de Camargo and a Pieros Sotiriou's header eleven minutes from time.

On 5 February 2017, APOEL extended their lead at the top to five points following their narrow 1–0 away win over Karmiotissa and the failure of their closest rivals AEL and Apollon to defeat their opponents.

With their Europa League tie against Athletic Bilbao at the back of their minds, APOEL managed to clinch the win thanks to a Facundo Bertoglio's goal in the 5th minute after an excellent combination with Efstathios Aloneftis.

Despite that, coach Thomas Christiansen rested six players ahead of the crucial UEFA Europa League round of 32 match against Athletic Bilbao, APOEL got an easy and well deserved victory.

On 4 March 2017, APOEL beat arch-rivals Omonia 2–1 at home and ended the regular season atop league standings, four points ahead of second placed AEK Larnaca.

On 1 April 2017, a late AEK Larnaca strike stunned leaders APOEL as they suffer a 1–2 defeat and their advantage over second placed Apollon Limassol reduced to just four points.

On 30 April 2017, APOEL took a decisive step towards their fifth consecutive league title after beating 4–1 AEL at Limassol, while AEK defeated Apollon and remained four points behind the top.

On 7 May 2017, in the top-of-the-table clash, APOEL were held to a goalless draw by AEK Larnaca at the GSP Stadium and remained four points clear at the top of the league table, two matches before the end.

Six minutes into the second half, Georgios Efrem won a penalty which was converted by Pieros Sotiriou to give APOEL the lead, while substitute Vander added a third in stoppage time to secure another league title for his team.

On 5 April 2017, APOEL's coach Thomas Christiansen decided to rest several regular starters as his side held to a goalless draw by AEL Limassol in the first leg of their Cyprus Cup quarter-final meeting.

On 3 May 2017, despite fielding a team based only on reserve players, APOEL easily beat Doxa Katokopias 5–0 at the GSP Stadium and booked their place to the Cypriot Cup final.

[6] On 27 July 2016, APOEL suffered 2–1 loss to Rosenborg at Lerkendal Stadion, but the vital away goal gave the team a good chance and plenty of hope of reaching the play-off round of the competition.

APOEL's persistence rewarded in the first minute of the injury time when Vander's low cross picked out by Giannis Gianniotas at the far post who poked home what looked to be a certain winner.

Almost straight after kick-off, a mix-up in the Norwegian defense handed Tomás De Vincenti the chance to volley in from thirty yards with goal unguarded to send the home crowd into jubilation after an enduring night.

A goal two minutes before the break from Andrija Pavlović gave Copenhagen a narrow but deserved win, leaving APOEL with plenty of work to do in the return match in Nicosia.

On 24 August 2016, APOEL came very close to qualify for the UEFA Champions League group stage, before a late FC Copenhagen goal saw their hopes evaporate after a 1–1 draw at GSP Stadium.

But four minutes before the end and just as the game looked to be heading to the extra time, Federico Santander was given too much space in the area to pick out his spot and beat Boy Waterman with a swerving shot inside his near post.

On 3 November 2016, APOEL achieved an important 1–0 victory over Young Boys at GSP Stadium, which left them on the brink of qualification to the knockout phase of the Europa League.

Just before the hour mark, Marin Aničić levelled from close range after Boy Waterman fumbled his catch from a corner, and six minutes before the end Đorđe Despotović bundled in a second for the home side, after his initial attempt hit the post.

In the 83rd minute, Igor de Camargo slotted the ball home from close range after an accurate low cross from Nuno Morais to secure APOEL's decisive victory.

Despite being one of the seeded teams, APOEL handed a tough draw in the UEFA Europa League round of 32 as they were drawn to face Basque giants Athletic Bilbao.

Athletic piled on the pressure after the break, and scored two more goals until the 72nd minute, first with Aritz Aduriz who took advantage of a Cédric Yambéré's mistake and then with a close range header by Iñaki Williams.

APOEL piled on the pressure after the break and almost got the equalizer in the 87th minute when Vander hit the bar from a 40-yard free kick, but failed to score any goal and Anderlecht took a narrow advantage ahead of the next week's match in Belgium.

On 16 March 2017, APOEL were eliminated from the Europa League with their heads held high following a 0–1 defeat by Anderlecht at Constant Vanden Stock Stadium, bringing their memorable campaign to an end at the last-16 of the competition.

In the 65th minute, as happened in the first leg, APOEL's players gave the ball away in the middle of the field and Frank Acheampong struck from close range after a quick counterattack to give Anderlecht another narrow 1–0 win and a place to the quarter-finals of the competition.