The jets soared across the skies above Leuchars Station, RAF Tain and RAF Lossiemouth.
In the pilot’s seats were the Chief of the Air Staff and RAF Marham’s Station Commander, who were both conducting their final ever flights.
Hitting such a milestone meant the day ended with a very particular RAF tradition that they could not escape - the 'soaking'.
"It's a very significant moment for me personally, but I think more importantly, very significant for the RAF," Air Chief Marshal Sir Stephen Hillier told Forces News.
"This is after 37 years of frontline service - that's nearly 40% of the RAF's history with just this one aircraft.
"It's done such a fantastic job in operations around the world."
Over the past few days, thousands of people came out to show support, eagerly capturing the iconic jets on mobile phones across the country as local residents came out to take a glimpse of the aircraft.
On Tuesday, the jets were seen flying over RAF Cosford and several other locations including RAF Leeming, the National Memorial Arboretum and the BAE Systems site at Warton in Lancashire, where the Tornado was originally made.
At Warton – affectionately dubbed the Tornados' spiritual home – where many were built, thousands turned out to bid farewell.
After the planes flew over the site, Alan Thornber, who worked as part of the original team that developed the Tornado, told Forces News that the event was very important to him:
“It was brilliant, wasn’t it? I mean it was well worth waiting for! Up 40, 50 years I’ve waited for it I suppose.
“It was with sadness, with a touch of sadness. We wouldn’t really see the like of it again over this airfield.”
He said when the planes flew over he thought:
“What a great aircraft and how proud I have been to have been part of that programme for 50 years. It really was quite something.”
After over four years on Operation Shader, on 5 February this year the aircraft finally returned home from operations for good.
Another of the formation aircrew who had recently returned from operations will be Wing Commander Matt Bressani, the boss of 31 Squadron, the other remaining Tornado formation.
“The national response to the Tornado farewell campaign and the reception we received when we returned from operations earlier this month shows what a special place this aircraft has in the nation’s heart.”