The lifeboat's first big call came on a Sunday morning, 31 March 1940. The steamship Nydalen, running from Runcorn to Methil via Kirkwall, slammed at full speed onto a reef at Arinagour on the Isle of Coll. She was driven so hard aground that her own lifeboats could not be launched until high water. Captain Jensen and thirteen crew clustered in the open boats beneath her stern, waiting. Sir Arthur Rose arrived from Tobermory and lifted all fourteen men back to Arinagour. By then the war was reshaping the bay itself. HMS Western Isles, the Royal Navy's Anti-Submarine Training School, made Tobermory its flagship base. Its commander, Vice-Admiral Sir Gilbert Stephenson, was nicknamed the Terror of Tobermory for the merciless drills he inflicted on green crews bound for the Atlantic. Many of those Royal Navy personnel almost certainly crewed the lifeboat too.

When the war ended and the Navy left Tobermory, the lifeboat crew thinned out. By December 1947 the station could not find enough volunteers and was closed. The lifeboat was transferred to a new station at Mallaig on the mainland. With her went a small silver cross, a replica of St John's Cross of Iona, presented in 1940 by the Reverend George MacLeod, later Lord MacLeod of Fuinary, the founder of the Iona Community. The cross was supposed to be carried on every service launch from Tobermory. After the closure it sailed instead on the Mallaig boats for forty-three years, a small token of a station that no longer existed. Tobermory's harbour stayed busy with fishing boats and yachts, but the orange hull was gone.

By 1990, leisure sailing in the Hebrides had exploded. Yachts crowded the Sound of Mull. Mishaps multiplied. A local campaign argued that Tobermory needed its own lifeboat again, and the RNLI agreed. The first replacement boat, Ralph and Joy Swan, went on service that year, replaced the next year by the larger City of Bradford IV. On 26 May 1991, the Mallaig lifeboat stopped at Tobermory and, in a ceremony at the pier, handed back the silver Iona cross. It would once again sail on every Tobermory call-out. Two years later, the station bought a row of five lock-up garages by Mishnish Pier and converted them into proper crew quarters, an office for the Coastguard, and a workshop. The £61,000 appeal that paid for it was launched in memory of Bobby MacLeod, a veteran of the 1947 crew who had spent his last years campaigning for the station's return.

The current lifeboat, the all-weather 17-39 Elizabeth Fairlie Ramsey, has been on station since 2003. On 27 January 2013 she answered a call from a fishing boat with a failed gearbox seven miles west of Coll. The lifeboat hauled the boat toward Tiree, where another vessel was waiting to take up the tow. The rope parted. The fishing boat drifted onto rocks. Lines went out again, came taut, parted, went out again. After eleven hours of work in the winter dark, the lifeboat finally brought the boat safely back to Tobermory. That single rescue captures the rhythm of a Hebridean lifeboat station: long quiet weeks, then a call, then hours of cold, methodical work on a black sea, then the boat returning to the painted harbour at dawn.