The airline was formally established in 2001 (but had been operating since 1999 as a small operation) by Le Cocq's Stores in Alderney and was initially known as Le Cocq's Airlink.
It started operations carrying perishable goods from Bournemouth in the south of England to the island of Alderney.
Scheduled services were added on the same route on 1 February 2002.
The trading name Rockhopper was adopted on 29 August 2003.
In 2004, ownership changed to Healthspan Leisure and in 2005, Jetstream aircraft were added to the fleet.
The company moved its main operating base from Alderney to Jersey in January 2006.
Its headquarters is now at Healthspan House, The Grange, St. Peter Port, Guernsey.
The airline is wholly owned by the Healthspan Group.
The company changed the trading name from Rockhopper to Blue Islands on 14 February 2006.
This move coincided with the delivery of the first of its new fleet of 19-seater BAe Jetstream 31 aircraft and a new air link with the Isle of Man.

The deployment of the BAe Jetstream aircraft on some Guernsey-Jersey services meant Blue Islands gained a majority share of the market from its competitor (according to Airliner World magazine), helped by the introduction of an hourly shuttle service between Guernsey and Jersey known as the Blue Shuttle.
In December 2007, Blue Islands' share of the inter-island market was estimated to be over 50%, and in December 2009 its market share had risen to 68%.
Blue Islands went on to launch new routes from the Channel Islands to Beauvais–Tillé (ceased July 2008), Southampton, Geneva and Zurich.
A Dornier 328-110 (leased from ScotAirways) was added to the fleet in 2007.
However, by late 2010 its market share on the Guernsey-Jersey route had fallen to below 50% and its main competitor Aurigny was regaining much ground in the Channel Islands market.

In 2010, the airline added an ATR 42-320 to its fleet.
It emerged in July 2010 that Blue Islands had launched a bid with the States of Guernsey to buy its competitor, Aurigny.
This caused much controversy in the Channel Islands, and a Facebook page in opposition to the proposed buy-out gained nearly 600 members.
Those in favour of the deal claimed that it did not make sense for the two individual airlines to continue to make such large losses whilst operating in competition with each other.
The failure of the deal was announced on 14 September 2010, amidst doubts over the security of Guernsey's slots at Gatwick Airport.

A number of changes took place in 2011.
Rob Veron was appointed as managing director and the Trislander fleet was repainted and refitted for a planned new hub at Alderney with routes to Southampton and Cherbourg, however the application was denied because the start date was within six months of the application date.
Blue Islands announced that a full withdrawal from Alderney would take place on 9 May 2011 (coincidentally Liberation Day), after 11 years of services.

In March 2011, it announced a twice-daily weekday route (with a once-daily flight on Sundays) from Jersey to London City Airport, and in April a route to Bristol was announced.
Daily services were announced between Jersey and Manchester Airport in September, along with the restoration of a thrice-weekly service to Bournemouth Airport, in competition with the airline's own more regular services to Southampton, as well as those of Flybe.
 In November the planned retirement of the Trislander fleet was made public, with the last day of operations to be 4 December.
This was because they were 'too noisy, old and small'.

On 16 June 2012, a Blue Islands ATR 42-300 registered G-DRFC operating from Guernsey to Jersey suffered a collapse of the left main landing gear while exiting the runway.
None of the 43 people on board were injured in the accident.
Blue Islands applied to the States of Guernsey for a licence to operate a twice-daily Guernsey-Bristol service in competition with Aurigny.
A licence hearing was due to take place in January 2013 regarding the application.
The application was withdrawn as Blue Islands wishes to concentrate on building the
The airline was formally established in 2001 (but had been operating since 1999 as a small operation) by Le Cocq's Stores in Alderney and was initially known as Le Cocq's Airlink. It started operations carrying perishable goods from Bournemouth in the south of England to the island of Alderney. Scheduled services were added on the same route on 1 February 2002. The trading name Rockhopper was adopted on 29 August 2003. In 2004, ownership changed to Healthspan Leisure and in 2005, Jetstream aircraft were added to the fleet. The company moved its main operating base from Alderney to Jersey in January 2006. Its headquarters is now at Healthspan House, The Grange, St. Peter Port, Guernsey. The airline is wholly owned by the Healthspan Group. The company changed the trading name from Rockhopper to Blue Islands on 14 February 2006. This move coincided with the delivery of the first of its new fleet of 19-seater BAe Jetstream 31 aircraft and a new air link with the Isle of Man.
The deployment of the BAe Jetstream aircraft on some Guernsey-Jersey services meant Blue Islands gained a majority share of the market from its competitor (according to Airliner World magazine), helped by the introduction of an hourly shuttle service between Guernsey and Jersey known as the Blue Shuttle. In December 2007, Blue Islands' share of the inter-island market was estimated to be over 50%, and in December 2009 its market share had risen to 68%. Blue Islands went on to launch new routes from the Channel Islands to Beauvais–Tillé (ceased July 2008), Southampton, Geneva and Zurich. A Dornier 328-110 (leased from ScotAirways) was added to the fleet in 2007. However, by late 2010 its market share on the Guernsey-Jersey route had fallen to below 50% and its main competitor Aurigny was regaining much ground in the Channel Islands market.
In 2010, the airline added an ATR 42-320 to its fleet. It emerged in July 2010 that Blue Islands had launched a bid with the States of Guernsey to buy its competitor, Aurigny. This caused much controversy in the Channel Islands, and a Facebook page in opposition to the proposed buy-out gained nearly 600 members. Those in favour of the deal claimed that it did not make sense for the two individual airlines to continue to make such large losses whilst operating in competition with each other. The failure of the deal was announced on 14 September 2010, amidst doubts over the security of Guernsey's slots at Gatwick Airport.
A number of changes took place in 2011. Rob Veron was appointed as managing director and the Trislander fleet was repainted and refitted for a planned new hub at Alderney with routes to Southampton and Cherbourg, however the application was denied because the start date was within six months of the application date. Blue Islands announced that a full withdrawal from Alderney would take place on 9 May 2011 (coincidentally Liberation Day), after 11 years of services.
In March 2011, it announced a twice-daily weekday route (with a once-daily flight on Sundays) from Jersey to London City Airport, and in April a route to Bristol was announced. Daily services were announced between Jersey and Manchester Airport in September, along with the restoration of a thrice-weekly service to Bournemouth Airport, in competition with the airline's own more regular services to Southampton, as well as those of Flybe.  In November the planned retirement of the Trislander fleet was made public, with the last day of operations to be 4 December. This was because they were 'too noisy, old and small'.
On 16 June 2012, a Blue Islands ATR 42-300 registered G-DRFC operating from Guernsey to Jersey suffered a collapse of the left main landing gear while exiting the runway. None of the 43 people on board were injured in the accident. Blue Islands applied to the States of Guernsey for a licence to operate a twice-daily Guernsey-Bristol service in competition with Aurigny. A licence hearing was due to take place in January 2013 regarding the application. The application was withdrawn as Blue Islands wishes to concentrate on building the 
Blue Islands