Aurigny’s flagship jet, the Embraer 195, was caught in a thunderstorm on Thursday at about 11:15 BST.
Flight GR605 was able to land normally and no-one was injured, Aurigny Air Services said.
The airline did not to say how many passengers were on board, but it said the plane was grounded while engineers inspected minor damage to its tail.
Heavy rain and storms have been spreading across much of England, causing flooding and travel problems.
An airline spokesman said: “We were cleared to land by air traffic control and no other aircraft, operating in the same conditions, were similarly affected. Our aircraft landed normally and no-one was injured or adversely affected in any way.”
It chartered replacement aircraft to get passengers to and from London Gatwick on Thursday evening, but some passengers complained on Twitter about a nine-hour hold up.
Dave Brooks, abandoned his trip after waiting at Gatwick for four hours, claiming there was “poor communication, delayed refreshments, no contingency plan”.
A company spokesman said one of its ATR72 aircraft was operating the route on Thursday at full capacity, “but due to its size, 72 versus 122 seats, it could not accommodate all the passengers booked to fly on the Embraer sectors”.
“We issued refreshment vouchers at Gatwick and we kept passengers informed… we got back as many passengers as we could,” the company said.
Flights on Friday were further disrupted by fog, which stopped flights in or out of the Channel Islands until about 13:00 BST.
Aurigny said it had charted two planes to replace the grounded jet.