The RN's final order was for 44 ASW aircraft, originally designated Merlin HAS.1 but soon changed to Merlin HM1. The first fully operational Merlin was delivered on 17 May 1997, entering service on 2 June 2000. All aircraft were delivered by the end of 2002, and are operated by four Fleet Air Arm squadrons: 814 NAS, 820 NAS, 824 NAS and 829 NAS, all based at RNAS Culdrose in Cornwall. 700 NAS was the Merlin Operational Evaluation Unit from 2000 to 2008. In March 2004, Navy Merlins were temporarily grounded following an incident at RNAS Culdrose in which a tail rotor failed due to a manufacturing defect. An improved tail rotor was designed and adopted on most AW101s; according to AgustaWestland the redesigned rotor also significantly reduced associated maintenance.

The Merlin HM1 has been cleared to operate from the Royal Navy's aircraft carriers, amphibious assault ships, Type 23 frigates and several Royal Fleet Auxiliary (RFA) vessels including the Fort Victoria class; it is also to equip the Type 45 destroyer. 30 aircraft were upgraded under the £850m Merlin Capability Sustainment Programme to Merlin HM2 standard. The MCSP added new mission systems, sensor upgrades and a digital cockpit The HM2 performed its first ship-borne test flight in September 2012. By August 2013, several Merlin HC2s had been delivered to 824 NAS, these are to begin operations in mid-2014. A total of 8 airframes did not receive the upgrades due to financial reasons, and instead shall be used in alternative roles.

On 15 December 2009, plans were announced to transfer RAF Merlin HC3s and HC3As to the Commando Helicopter Force to replace retiring Sea King HC4 helicopters. The Sea King is to retire in 2016, after which the Navy will operate a combination of the Wildcat and Merlin. It is intended that 846 NAS will reform with ex-RAF Merlin HC3s in 2015. 845 NAS will follow in 2017, operating the fully navalised Merlin HC4.

The Merlin has been considered as a replacement for the Sea King ASaC7 in the airborne early warning (AEW) role. In September 2011, Thales UK proposed re-using Sea King ASaC7 equipment, such as the Searchwater 2000, to provide AEW-configured AW101; Lockheed Martin has proposed developing a new multi-functional sensor for either the Merlin or other aircraft. In 1995, it was announced the Navy's Westland Lynx helicopters would be retired in favor of an all-Merlin fleet. however, the subsequent 2010 SDSR stated the future naval helicopters to be the Wildcat (a upgraded variant of the Lynx) and the Merlin.

Royal Navy Merlins have seen action in the Caribbean, on counter-narcotics and hurricane support duties, as well as maritime security duties in the Persian Gulf. Merlins have also seen active duty in Iraq, providing support to British and coalition forces based in the region.[

Eén uitvoering mogelijk;