The 2016–17 season is Exeter City's 115th year in existence and their fifth consecutive season in League Two. Along with competing in League Two, the club also participated in the FA Cup, EFL Cup and EFL Trophy. In September, Exeter City broke their all-time record for consecutive home league losses by losing their first five home matches of the season. Exeter City did not record their first league win at their home ground St James Park until mid-December, after 10 attempts. A dramatic upturn in form saw the team rise from the bottom of the league table to a high of 4th. From 31 December 2016 to 4 February 2017, Exeter have won all seven of their fixtures with David Wheeler scoring in each match. Wheeler equaled and then broke records set by Henry Poulter, Roderick Williams and Alan Beer with this feat. Another record was broken this season because no Exeter City team had ever won seven league games in a row (during the same season).

The season covered the period from 1 July 2016 to 30 June 2017.

On 19 May 2016, seven friendlies were announced on the club website. The majority were played against non-league West Country teams, but City also played Bristol Rovers, Burton Albion and a Cardiff City XI, the former of League One and the latter two of the Championship. City won all seven of the pre-season friendlies, conceding only two goals.

Exeter City began the season with an away fixture against Blackpool, which resulted in a 2–0 loss for the Grecians. Then followed two consecutive home fixtures, both of which the Grecians went on to lose. Against Hartlepool United, City were up 1–0 at half-time thanks to a 31st minute goal from Liam McAlinden, but conceded two goals within just two minutes in the final half-hour to lose 2–1. The Grecians also went down to a late goal four days later versus Crawley Town, when Josh Yorwerth scored in the 83rd minute. After these three opening losses, City were bottom of the table. Up next was a trip to Accrington Stanley, where the Grecians won their first league match thanks to two goals in a frantic six minutes in the second half. Ryan Harley opened the scoring for Exeter in the 66th minute before Arron Davies (who left Exeter City in the summer after his contract expired) equalised four minutes later. City were very quickly back ahead when Jake Taylor scored the winning goal in the 72nd minute. The Grecians lost their final August fixture at home to promotion-chasing Portsmouth because of an 85th-minute penalty, but City again failed to take their chances. City scored only three goals in August, picking up a mere three points from five matches. The Grecians sat in the relegation zone at 23rd place, ahead only of Cambridge United.

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