Spurs play Dortmund away in Germany on Tuesday in their last 16, return leg after thumping the Germans 3-0 in the first leg at Wembley.
However, Pochettino, 47, is far from happy with having a day less to prepare for the last 16 tie at Dortmund's Signal Iduna Park.
Spurs had a bruising 1-1 draw at home to Arsenal in Saturday's North London derby, while Dortmund lost 2-1 at Augsburg on Friday night in the Bundesliga.
"They played Friday, we played Saturday," said Spurs coach Pochettino.
"It's not fair to play with a massive disadvantage.
"We need help from the FA and the Premier League - for us it's impossible.
"We played (a Premier League game) on a Sunday before the first leg, which was on a Wednesday, when Dortmund played Saturday.
"Now we played Saturday, Dortmund played Friday.
"I don't know if the FA or the Premier League are to blame or television, who wanted us to play live Saturday or Sunday."
Pochettino pointed to the example of Stade Rennes, who postponed a French league game at the weekend to prepare for Thursday's Europa League, last 16 tie at home to Arsenal.
"Looked what happened to Rennes, they had a game cancelled the weekend game to held prepare to play Arsenal," said Pochettino.
"In Europe, the people are more sensitive to helping their clubs prepare for Europe, that's my point.
"I want us to have the same amount preparation time as our opponents.
"We need to change it in the future to help English clubs be stronger in the competition."
Spurs last reached the Champions League's quarter-finals in 2011 - losing 4-0 at Real Madrid and beaten 1-0 at home - and Pochettino knows this is a golden chance for Spurs.
Harry Kane is expected to lead Spurs' attack while Pochettino said Harry Winks and Eric Dier could feature after injuries.
The Argentinian repeatedly said Spurs must 'forget' their heavy first-leg win at Wembley and finish the job by seeing off a Dortmund team who have one win in seven games.
Son Heung-min and Kane scored at Dortmund when Spurs won 2-1 in the group stages in 2017/18 and Pochettino wants another convincing away win.
"The 3-0 at Wembley is not important.
"We need to forget the first leg, be very professional and win the game.
"We need to start at a very good level, be aggressive, fight from the beginning, high tempo.
"We know Dortmund are a good team, they deserve to be there and they are going to start aggressive and try to push us deeper - we need to be just as aggressive."