The retail giant said it will begin talks with affected staff in due course.
However, the firm added that it would put additional resources into its digital unit.
Boots president Simon Roberts said: “Together with my leadership team, I believe this plan will make Boots even better for our customers and drive sustainable future growth.”
It comes months after the mega-merger between owner Alliance Boots and US pharmacy group Walgreens.
About half of the cuts will fall at the firm’s UK head office in Beeston, Nottingham, and will include support and administrative staff.
In total the HQ has 4,000 staff, while the group employs 60,000 in the UK across nearly 2,500 stores.
The company said the purpose of the plan was to “bring together and simplify how resources are used”.
It added that it expects to achieve the cuts through a mixture of natural attrition, redeployment, retraining and redundancies.
Mr Roberts said: “We also remain fully committed to our presence in Nottingham, which has been the home of Boots since the very beginning.
“We have not taken these decisions lightly, and understand the impact that today’s announcement may have on our colleagues.”
In December Alliance Boots completed its mega-merger with America’s Walgreens.
It was announced in August that the US firm would take full control of the Boots the Chemist owner in a £9 billion cash and shares deal to swallow up the 55% of the company it did not already own.
The new group, Walgreens Boots Alliance, is based in Chicago but the headquarters of Boots remains in Nottingham, where its founder, John Boot, first opened a herbalist shop in 1849.
Walgreens has said a programme of cost-cutting would target one billion dollars (£600 million) of savings by 2017.
In March Boots also said it would cut 700 jobs after pulling the plug on 12 health and beauty outlets branded Wellbeing Services less than three years after the stores were