The 120 soldiers are the first of a total of 800 British troops to be stationed in Estonia for NATO's Enhanced Forward Presence operation, which was launched following Russia's reunification with Crimea.
They landed on Friday at the Amari airbase, 25 miles (40 km) southwest of the capital Tallinn.
British Defense Secretary Michael Fallon said this was the biggest UK military deployment in Europe since the end of the Cold War aimed at countering an "increasingly assertive Russia."
Fallon said the troop deployment was necessary "because of the increased Russian aggression that we've seen and the need to reassure our allies on the eastern side of NATO."
"British troops will play a leading role in Estonia and support our US allies in Poland, as part of wider efforts to defend NATO," he said.
Around 3,500 US troops arrived in Poland in January, one of the largest deployments of US forces in Europe since the end of the Cold War in 1991, sparking immediate anger from Russia.
The American troops are on a training mission in Poland before moving to other NATO member states in Eastern Europe for additional training exercises.
Russia has already described the positioning of NATO forces near its border as a threat.
The US and its NATO allies have been at odds with Moscow since Ukraine’s strategic Black Sea peninsula of Crimea rejoined Russia following a referendum in March 2014.
The troop deployments come as US President Donald Trump expressed Washington’s "strong support" for NATO in a meeting with German Chancellor Angela Merkel on Friday.
However, Trump repeated his stance that NATO allies need to "pay their fair share" for the cost of military assistance. The new president claimed many countries owe "vast sums of money" but he declined to identify Germany as one of the nations.