Simon Stevens said there was a need to fight the “super-size snack culture” as he set a 250-calorie limit on sweets and chocolate sold in hospital canteens, shops and vending machines.
This means that most larger packs of chocolate and “grab bags” of sweets will be taken off the shelves, with NHS hospitals given a cash boost if they facilitate the move.
Hospital chiefs will need to ensure that 80% of items sold do not exceed the 250-calorie limit.
In April, NHS England also said sugary drinks will be banned from hospital shops next year unless action is taken to cut their sales.
Cans and bottles of sugary soft drinks are covered by that move, as well as sugary drinks made in NHS cafes and canteens such as coffees with sugar syrup.
Other drinks affected are those with added sugar, including fruit juices with extra sugar, and sugary milk drinks, depending on their total milk content.
Mr Stevens said: “The NHS is now stepping up action to combat the super-size snack culture which is causing an epidemic of obesity, preventable diabetes, tooth decay, heart disease and cancer.
“In place of calorie-laden, sugary snacks we want to make healthier food an easy option for hospital staff, patients and visitors.”
The NHS has pledged to boost the sale of healthy foods and end promotions of sugary and fatty or salty foods at checkouts.
It has ruled that 75% of pre-packed sandwiches and other savoury pre-packed meals must be 400 calories or less, and must not exceed 5g of saturated fat per 100g.
Some 80% of drinks must also have less than 5g of added sugar per 100ml.
It has also targeted NHS staff, including those who struggle to access healthy food while on overnight shifts.
Almost 700,000 NHS employees out of 1.3 million are thought to be overweight or obese.
Dr Alison Tedstone, chief nutritionist at Public Health England, said: “Hospitals have an important role in addressing obesity - not just treating those suffering the consequences, but helping to prevent it in the first place.
“Any plans to offer healthier food are a positive step towards tackling the country’s obesity problem.”
Andrew Roberts, business enterprise manager for Royal Voluntary Service, said that in the first quarter of 2017 its outlets had seen year-on-year sales of fruit increase by 25%, healthier chilled snacks like salad and sushi by 55% and healthier sweet and savoury snacks like popcorn and dried fruit by 109%.
He added: “We will be implementing these new guidelines and are hopeful that they will result in healthier food being a more consistent feature in all hospital retailers.”