The Football Association Premier League Ltd (FAPL) is operated as a corporation and is owned by the 20 member clubs. Each club is a shareholder, with one vote each on issues such as rule changes and contracts. The clubs select a chairman, chief executive, and board of directors to oversee the daily operations of the league. The Football Association is not directly involved in the day-to-day operations of the Premier League, but has veto power as a special shareholder during the election of the chairman and chief executive and when new rules are adopted by the league.

The current chief executive is Richard Masters, who was appointed in December 2019. The chair is currently Alison Brittain, who took over the role in early 2023.

The Premier League sends representatives to UEFA's European Club Association, the number of clubs and the clubs themselves chosen according to UEFA coefficients. For the 2023–24 season, the Premier League has 13 representatives in the Association: Arsenal, Aston Villa, Brighton & Hove Albion, Chelsea, Everton, Liverpool, Manchester City, Manchester United, Newcastle United, Nottingham Forest, Tottenham Hotspur, West Ham United, and Wolverhampton Wanderers. The European Club Association is responsible for electing three members to UEFA's Club Competitions Committee, which is involved in the operations of UEFA competitions such as the Champions League and UEFA Europa League.
The Premier League has faced criticism of its governance due to an alleged lack of transparency and accountability.

Following the Premier League's blocking of the attempted takeover of Newcastle United by a PIF-backed consortium through the league's Owners' and Directors' test, many MPs, Newcastle United fans and related parties to the deal denounced the Premier League for its perceived lack of transparency and accountability throughout the process. On 6 July 2021, consortium member Amanda Staveley of PCP Capital Partners said that "fans surely deserve absolute transparency from the regulators across all their processes – to best ensure that they act responsibly. They (the Premier League) are performing a function like that of a government regulator – but without the same systems for accountability."

On 22 July 2021, Tracey Crouch MP – chair of the fan-led review into the UK's football governance – announced in the review's interim findings that the Premier League had "lost the trust and confidence" of fans. The review also recommended that a new independent regulator be created to oversee matters such as club takeovers.

Premier League chief executive Richard Masters had earlier spoken out against the implementation of an independent regulator, saying in May 2021, "I don't think that the independent regulator is the answer to the question. I would defend the Premier League's role as regulator of its clubs over the past 30 years."

There are 20 clubs in the Premier League. During the course of a season (from August to May) each club plays the others twice (a double round-robin system), once at their home stadium and once at that of their opponents, for 38 games. Teams receive three points for a win and one point for a draw. No points are awarded for a loss. Teams are ranked by total points, then goal difference, and then goals scored. If still equal, teams are deemed to occupy the same position. If there is a tie for the championship, for relegation, or for qualification to other competitions, the head-to-head record between the tied teams is taken into consideration (points scored in the matches between the teams, followed by away goals in those matches.) If two teams are still tied, a play-off match at a neutral venue decides rank.
A system of promotion and relegation exists between the Premier League and the EFL Championship. The three lowest placed teams in the Premier League are relegated to the Championship, and the top two teams from the Championship promoted to the Premier League, with an additional team promoted after a series of play-offs involving the third, fourth, fifth and sixth placed clubs. The number of clubs was reduced from 22 to 20 in 1995, when four teams were relegated from the league and only two teams promoted. The top flight had only been expanded to 22 teams at the start of the 1991–92 season – the year prior to the formation of the Premier League.

On 8 June 2006, FIFA requested that all major European leagues, including Italy's Serie A and Spain's La Liga, be reduced to 18 teams by the start of the 2007–08 season. The Premier League responded by announcing their intention to resist such a reduction. Ultimately, the 2007–08 season kicked off again with 20 teams.
Video assistant referee (VAR), was introduced to the Premier League at the beginning of the 2019–20 season. It uses technology and officials to assist the referee in making decisions on the pitch. However, its use has been met with mixed receptions from fans and pundits, with some praising its accuracy whilst others criticise its impact on the flow of the game and consistency of decision-making.

The on-field referee still makes the final decision, but VAR can assist the referee in the decision-making process. VAR can only be used for four types of decisions: goals, penalty decisions, direct red card incidents, and cases of mistaken identity. VAR officials review the video footage and communicate with the on-field referee via a headset. The VAR officials are located in a central control room, which is equipped with multiple camera angles and the ability to replay footage at various speeds.

A study evaluating fan reception of VAR in the Premier League was made by Otto Kolbinger and Melanie Knopp and was done by analysing Twitter data. The researchers used sentiment analysis to measure the overall positive or negative attitudes towards VAR, as well as topic modelling to identify specific issues that fans are discussing related to VAR. The study found that the reception of VAR on Twitter is largely negative, with fans expressing frustration and criticism of the technology's impact on the flow of the game and the inconsistency of decisions. The researchers also identified specific issues, such as handball and offside decisions, that fans are particularly critical of. The study concludes tha…

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Fifty-one clubs have played in the Premier League from its inception in 1992, up to and including the 2023–24 season.
Italics indicate former Premier League champions that are currently outside the Premier League.
Twenty clubs are competing in the 2024–25 season – top seventeen from the previous season and three promoted from the Championship.
• Luton Town, Burnley and Sheffield United were relegated to the EFL Championship for the 2024–25 season, whilst Leicester City, Ipswich Town, and Southampton, as winners, runners-up and play-off final winners, respectively, were promoted from the 2023–24 season.
• Only two clubs have remained in the Premier League since their first promotion: Brentford and Brighton & Hove Albion, who have been in 4 and 8 season(s) (out of 33), respectively.
199 ^ Founding member of the Premier League
299 ^ Never been relegated from the Premier League
399 ^ Reduced from 106 seasons due to WW2.
499 ^ One of the original twelve Football League teams
In 2011, after Swansea City gained promotion, a Welsh club participated in the Premier League for the first time. The first Premier League match to be played outside England was Swansea City's home match at Liberty Stadium against Wigan Athletic on 20 August 2011. The number of Welsh clubs in the Premier League increased to two in 2013–14, as Cardiff City gained promotion, but they were relegated after their maiden season. Cardiff were promoted again in 2017–18 but the number of Welsh clubs remained the same for the 2018–19 Premier League season, as Swansea City had been relegated from the Premier League in 2017–18. Following Cardiff City's relegation after the 2018–19 season, there are currently no Welsh clubs participating in the Premier League.

Because they are members of the Football Association of Wales (FAW), the question of whether clubs like Swansea should represent England or Wales in European competitions has caused long-running discussions in UEFA. Swansea took one of England's three available places in the Europa League in 2013–14 by winning the League Cup in 2012–13. The right of Welsh clubs to take up such English places was in doubt until UEFA clarified the matter in March 2012, allowing them to participate.

Participation in the Premier League by some Scottish or Irish clubs has sometimes been discussed, but without result. The idea came closest to reality in 1998, when Wimbledon received Premier League approval to relocate to Dublin, Ireland, but the move was blocked by the Football Association of Ireland. Additionally, the media occasionally discusses the idea that Scotland's two biggest teams, Celtic and Rangers, should or will take part in the Premier League, but nothing has come of these discussions.