Weber left Gotha on 20 December with the intention of undertaking another extended tour, which he opened on 1 January 1813 with the première of the hymn and the first public performance of the new concerto at the Gewandhaus in Leipzig. On 12 January he arrived in Prague, ostensibly on the way to Vienna and thence to Italy. But the tour did not continue beyond the Bohemian capital, as the administrators of the Estates Theatre offered him the position of Musikdirektor in the hope that he would revive the moribund opera. Forgoing his dream of Italy, in part so that he could discharge his outstanding debts and in part because he relished the opportunity to shape an institution according to his own vision, Weber accepted the appointment for three and a half years at an annual salary of 2000 gulden and with provision for yearly benefit performances and annual leaves. With the dissolution of the old company at Easter 1813, Weber went to Vienna at the end of March to recruit new singers, choristers and orchestra players. There he also encountered Baermann, Meyerbeer, Vogler and Spohr, and presented a concert on 25 April at the Redoutensaal.
Despite the orchestra's initial resistance to Weber and the difficulties of putting together a new company – compounded by wartime conditions that kept some potential cast members from travelling to Prague – the opera was able to start again on 9 September 1813 with a German-language performance of Spontini's Fernand Cortez, the first of the 72 works and approximately 430 performances given during Weber's tenure (Bužga, L1985). As he had in Breslau, Weber attempted an ambitious repertory of original German works and French and Italian operas in translation. But for reasons outside his control the company never fully attained the goals he set. Although the theatre boasted a fine orchestra and a great dramatic soprano in Therese Grünbaum, Weber was unable to cast classics like Die Zauberflöte and Die Entführung aus dem Serail, or any of Gluck's operas. Nevertheless, under Weber the Prague theatre did perform such difficult works as Beethoven's Fidelio, Cherubini's Faniska, Poissl's Athalia and Meyerbeer's Wirth und Gast (later known as Alimelek), and it gave the première of Spohr's Faust (1 September 1816).
For a number of reasons Weber never really enjoyed his tenure in Prague. His heavy workload doubtless contributed to the frequent bouts of ill-health during these years, illnesses that weakened a constitution already exhibiting symptoms of tuberculosis. Weber quickly came to feel isolated in Prague; despite a good friendship with the amateur cellist Dr Philipp Jungh, he failed to find a congenial circle of artists and intellectuals with whom he could associate and make music. In his letters he frequently complained about the Prague audiences, which he found generally unresponsive. A particularly volatile personal life also contributed to his misery. By the end of 1813 Weber was embroiled in a doomed relationship with a married actress, Therese Brunetti, from which he extracted himself in spring 1814 with the start of a romantic involvement with the singer Caroline Brandt, a popular member of his company. Weber eventually married Caroline, in 1817, but the early years of the courtship were stormy, as her jealousy and quick temper, her justified pride in her own career and her mother's initial disapproval of Weber provided ample grounds for frequent dissonance in a relationship that admittedly is illuminated only from Weber's side by his diary and the many surviving letters that he wrote to her (Bartlitz, D1986). The relationship faltered in summer 1815 when the couple agreed to separate prior to Weber's annual leave, but by June 1816 they were fully reconciled and by the end of 1816 they were betrothed.
With such distractions, it is not surprising that Weber found it difficult to compose in Prague. The strong desire to write a new opera was repeatedly thwarted by his inability to obtain a suitable text, as a call for librettos that he published in the Allgemeine musikalische Zeitung in March 1813 yielded no viable subjects. More fruitful for composition were the summer vacations that afforded him the chance to restore health and spirits. In summer 1814 Weber went to Bad Liebenwerda for a three-week cure before moving on to Berlin for nearly five weeks to enjoy the company of his old friends. The vacation concluded with another stay with Duke Emil Leopold at Gotha and Schloss Gräfentonna, where, with the celebrations surrounding the victorious return of the King of Prussia to Berlin fresh in his mind, Weber began to compose the first pieces that won him widespread acclaim, the six songs for unaccompanied male chorus Leyer und Schwerdt (op.42) on patriotic poems by Theodor Körner.
In summer 1815 Weber spent most of his leave in Munich reunited with Baermann. At first unable to concentrate because of his recent breakup with Caroline Brandt (with whom he nevertheless continued a painful correspondence), he eventually began to compose again, writing two movements of the Grand duo concertant for Baermann and himself and a concert aria for the soprano Helene Harlas. In Munich patriotic fervour once again stimulated artistic creation, as Weber's experience of public celebration of the allied victory at Waterloo engendered a plan for a cantata entitled Kampf und Sieg. After a concert in Munich on 2 August and one in Augsburg on 8 August, Weber remained in Munich in relative seclusion to work on the cantata, complete the Clarinet Quintet, which he had started in 1811, and revise the Horn Concertino for the horn player Sebastian Rauch.
By the time of his return to Prague on 7 September 1815 Weber had decided to terminate his association with the Estates Theatre at the end of his contract in September 1816. Although he continued to fulfil his duties conscientiously, his activities during the last year in Prague broadened considerably. He returned to literary activity, writing not only concert reviews for the k.k. priv. Prager Zeitung, but also ‘dramatic-musical notices’, brief historical-critical essays designed to enhance the public appreciation of new works in the Prague repertory. His reading in February 1816 of the fourth part of E.T.A. Hoffmann's Fantasiestücke in Callots Manier prompted him to resume his own novel, and two Prague concerts given by Hummel in April encouraged him to apply himself again to the piano. After the première of Kampf und Sieg on 22 December 1815, Weber set about systematically to send manuscript copies of the score to the allied monarchs in the hope of financial reward and a possible appointment. From this resulted permission to perform the cantata in Berlin. Weber went there in early June 1816 and the success of the performances on 18 and 23 June fuelled the efforts – ultimately unsuccessful – of the Intendant of the royal Prussian theatre, Count Carl von Brühl, to secure a court appointment for Weber. On his way back to Prague, Weber spent four days (13–17 July) in Carlsbad (now Karlovy Vary), where the Intendant of the royal Saxon theatre, Count Heinrich Vitzthum von Eckstädt, approached him about directing a new German-language opera company that the court hoped to establish in Dresden.
In his last weeks in Prague Weber conducted the première of Spohr's Faust, prepared a number of organizational aids for his successor, and cleared his debt to his creditors in Stuttgart. By this time he could entertain serious hopes for a position in Dresden, for on 19 August he had accepted Vitzthum's terms: an appointment as Kapellmeister at a salary of 1500 thalers with primary responsibility for the German opera but with responsibilities as well for music at the court church and the Italian opera. However, official confirmation of the appointment was slow to come, as the Dresden court was cautious about committing resources to the new venture. Conducting his last performance on 30 September, Weber left Prague on 7 October, with plans to go to Berlin and from there (if no news arrived from Dresden) on an extended tour of northern Germany and Denmark.
Weber arrived in Berlin on 13 October, accompanied by Caroline Brandt, who had been engaged for guest appearances at the theatre, and her mother. There Weber composed or completed the second and third piano sonatas, three volumes of songs (opp.43, 46 and 47), and the Grand duo concertant. The stay in Berlin exposed Weber to E.T.A. Hoffmann's Undine, which stimulated his most important opera review, and witnessed two events that were to change the rest of his life. On 19 November, the eve of Caroline's departure from Berlin, she and Weber became engaged, and on 25 December Weber at last received a letter from Vitzthum confirming the new appointment and requesting him to come to Dresden as quickly as possible.