Brain tumour patient Ashya King is expected to undergo his first consultation later at a Czech clinic ahead of planned proton beam treatment.
He was flown to Prague by private jet from Spain, where he was in hospital.
Parents Brett and Naghemeh King removed the five-year-old from Southampton General Hospital on 28 August after disagreeing with doctors.
The Proton Therapy Center says the treatment is suited to Ashya's type of brain cancer, medulloblastoma.
Ashya is now in the University Hopsital Motol in the Czech capital.
His father was due to meet doctors at the Proton Therapy Centre in Prague to discuss treatment options.
Meanwhile, Mr Justice Baker has given details about the ruling he made on Friday to allow Ashya's parents to take him to Prague to receive the proton beam treatment.
He said Mr and Mrs King, who were initially arrested after taking him out of hospital in Southampton, "were in the best position" to make decisions about the treatment options, where both courses were reasonable.
He added Portsmouth City Council officials had acted correctly in asking the High Court to assume responsibility for Ashya.
The boy is now no longer a ward of court.
The therapy centre said that documentation from the hospital in Malaga was reviewed before Ashya could travel.
The centre said an expert panel of physicians met earlier to discuss transportation details and additional treatment needed according to Ashya's current health.
Vladimir Vondracek, from the centre, said: "We will be targeting just the whole brain in the first phase and the spinal cord.
"The second phase will be targeting the back of the tumour, which was removed by surgery."
The treatment Ashya is due to receive in Prague is a type of radiation therapy that uses beams of protons - or small parts of atoms - rather than high energy X-rays, as with conventional radiotherapy.
The protons can be directed at a tumour more precisely than X-rays and unlike conventional treatments the beams stop once they hit the target, rather than carrying on through the body.
At the scene
Nick Beake, Correspondent
As the latest planeload of holidaymakers touched down on the coast of the Costa del Sol, one British family which has been so desperate to leave finally got their wish.
At 09:40 (local time) the private plane carrying Ashya King and his parents soared into the bright morning sunshine, destined for Prague.
The family's stay in Spain has now ended, but their arrival in the Czech Republic will be marked with equally strong interest.
This has been a story of medical disagreement, courtroom wrangling and impassioned public debate all played out across international borders.
But at its heart is a seriously ill little boy and his ongoing fight to beat cancer.
Ashya previously had major surgery to successfully remove a brain tumour on 24 July and a further operation on his brain on 22 August.
As a result of these procedures he was unable to speak, eat or drink on his own, and relied on a food pump.
Following his disappearance from Southampton Hospital, Hampshire Constabulary obtained a European arrest warrant on the grounds the Kings had neglected their son.
The couple were arrested in Spain and spent several days in custody.
But the Crown Prosecution Service (CPS) later withdrew the warrant and they were freed.
Ashya was also made a ward of court after an application was made by Portsmouth City Council - but a judge has ruled the wardship had been discharged as Ashya has been admitted to hospital in Prague.
Legal judgement on Ashya case
Clive Coleman, legal affairs correspondent
Mr Justice Baker has said he could not make a judgment on who was correct about the accounts of the dispute between Ashya's parents and the Southampton Hospital as he hadn't had a statement from the parents.
He also said Portsmouth City Council had been correct to apply for Ashya to become a ward of court based on the medical evidence it had at the time about Ashya's medical condition and the risks he faced.
However, he described Brett and Naghemeh King as "loving parents", and said "it was not in Ashya's best interests to have been separated" from them.
The judge said that there are cases where parents are seeking unreasonable medical treatment, but that this was not the case.
He said the parents "were in the best position" to make decisions about the treatment options, where both courses were reasonable.