Ukad, which carries out testing on behalf of the Football Association, took 1,204 samples from 1,989 players to appear in the EFL in 2015-16.
From 550 players to play in the Premier League, 799 samples were taken. There were no tests in the National League.
These figures do not account for players being tested more than once.
That means one player being tested five times would account for five samples, while some samples may have been taken from players who were registered with clubs but did not make a first-team appearance.
The figures, released under the Freedom of Information Act, show only 36 samples were taken from 169 players to appear in Women's Super League One - the top flight of domestic women's football in England - meaning at least 78% of players were not tested.
The Football Association said in a statement that "like any sport" it prioritised its anti-doping programme "at the elite end".
It added: "This applies not just to staggering downwards the number of tests per competition but also in terms of focusing attention around those players playing the most number of first-team minutes.
"In addition, the anti-doping programme is research and intelligence-led, meaning any player the FA believes presents a particular doping risk will be targeted."
A spokesperson for Ukad told BBC Sport: "Like all sports, we create and deliver a testing programme for football which places resources where they are most effective in order to target where we believe the greatest risk of doping lies.
"But anti-doping programmes are no longer focused solely on testing and test numbers. There are 10 anti-doping rule violations under the World Anti-Doping (Wada) code, of which the presence of a prohibited substance in a sample is just one."
While there were more samples obtained than players who appeared in the Premier League during 2015-16, the ratio of samples to players tested across the three divisions making up the EFL was far lower:
- In the Championship, 540 samples were taken from 689 players to make a minimum of one appearance last season, meaning at least 21% were not tested.
- In League One, 347 samples were taken from 742 players to make an appearance, meaning at least 53% of players were not tested.
- In League Two, 317 samples were taken from 749 players to make an appearance, meaning at least 57% of players were not tested.
These figures do not include samples collected from under-18 and under-21 squads or from national squads, while any players or teams competing in European competition are also subject to Uefa's anti-doping programmes.
According to Ukad, which says every anti-doping rule violation is listed on its website, Brentford midfielder Alan Judge was the only player in England and Wales tested on behalf of the FA to breach doping regulations during the 2015-16 season - an offence for which he was reprimanded.
The samples taken by Ukad, the only organisation that drug tests on behalf of the FA, are tested for both performance-enhancing and recreational drugs. The FA says there were three failed tests by unnamed players for recreational drugs last season.